Picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Picard Metrics Definitions
Click on a metric to see a description of its fields.
- AlignmentSummaryMetrics: High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
- BaseDistributionByCycleMetrics:
- ClusteredCrosscheckMetric: A Metric class to hold the result of clustered crosschecking fingerprints.
- CollectHiSeqXPfFailMetrics.PFFailDetailedMetric: a metric class for describing FP failing reads from an Illumina HiSeqX lane *
- CollectHiSeqXPfFailMetrics.PFFailSummaryMetric: Metrics produced by the GetHiSeqXPFFailMetrics program.
- CollectOxoGMetrics.CpcgMetrics: Metrics class for outputs.
- CollectQualityYieldMetrics.QualityYieldMetrics: A set of metrics used to describe the general quality of a BAM file
- CollectRawWgsMetrics.RawWgsMetrics:
- CollectVariantCallingMetrics.VariantCallingDetailMetrics: A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
- CollectVariantCallingMetrics.VariantCallingSummaryMetrics: A collection of metrics relating to snps and indels within a variant-calling file (VCF).
- CollectWgsMetrics.WgsMetrics: Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage: Metrics for evaluating the performance of whole genome sequencing experiments.
- CrosscheckMetric: A class to hold the result of crosschecking fingerprints.
- DuplicationMetrics: Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
- ErrorSummaryMetrics: Summary metrics produced by CollectSequencingArtifactMetrics as a roll up of the context-specific error rates, to provide global error rates per type of base substitution.
- ExtractIlluminaBarcodes.BarcodeMetric: Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
- FingerprintingDetailMetrics: Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
- FingerprintingSummaryMetrics: Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
- GcBiasDetailMetrics: Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
- GcBiasMetrics:
- GcBiasSummaryMetrics: High level metrics that capture how biased the coverage in a certain lane is.
- GenotypeConcordanceContingencyMetrics: Class that holds metrics about the Genotype Concordance contingency tables.
- GenotypeConcordanceDetailMetrics: Class that holds detail metrics about Genotype Concordance
- GenotypeConcordanceSummaryMetrics: Class that holds summary metrics about Genotype Concordance
- HsMetrics:
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
- IlluminaBasecallingMetrics: Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
- IlluminaLaneMetrics: Embodies characteristics that describe a lane.
- IlluminaPhasingMetrics: Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
- IndependentReplicateMetric: A class to store information relevant for biological rate estimation
- InsertSizeMetrics: Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
- JumpingLibraryMetrics: High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
- MendelianViolationMetrics: Describes the type and number of mendelian violations found within a Trio.
- MergeableMetricBase: An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated.
- MultilevelMetrics:
- RnaSeqMetrics: Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
- RrbsCpgDetailMetrics: Holds information about CpG sites encountered for RRBS processing QC
- RrbsSummaryMetrics: Holds summary statistics from RRBS processing QC
- SequencingArtifactMetrics.BaitBiasDetailMetrics: Bait bias artifacts broken down by context.
- SequencingArtifactMetrics.BaitBiasSummaryMetrics: Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
- SequencingArtifactMetrics.PreAdapterDetailMetrics: Pre-adapter artifacts broken down by context.
- SequencingArtifactMetrics.PreAdapterSummaryMetrics: Summary analysis of a single pre-adapter artifact.
- TargetedPcrMetrics: Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
- UmiMetrics: Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
Note: Metrics labeled as percentages (with 'percent' in the full metric name or 'PCT' in the name given in the output file) are actually expressed as fractions. For example, 'PCT_TARGET_BASES_20X = 0.85' should be interpreted as '85 percent of targeted bases are covered to 20X coverage or more'.
AlignmentSummaryMetrics
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
| Field | Description |
|---|---|
| CATEGORY | One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair. |
| TOTAL_READS | The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters. |
| PF_READS | The number of PF reads where PF is defined as passing Illumina's filter. |
| PCT_PF_READS | The fraction of reads that are PF (PF_READS / TOTAL_READS) |
| PF_NOISE_READS | The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis. |
| PF_READS_ALIGNED | The number of PF reads that were aligned to the reference sequence. This includes reads that aligned with low quality (i.e. their alignments are ambiguous). |
| PCT_PF_READS_ALIGNED | The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS |
| PF_ALIGNED_BASES | The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence. |
| PF_HQ_ALIGNED_READS | The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong. |
| PF_HQ_ALIGNED_BASES | The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps. |
| PF_HQ_ALIGNED_Q20_BASES | The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher. |
| PF_HQ_MEDIAN_MISMATCHES | The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS). |
| PF_MISMATCH_RATE | The rate of bases mismatching the reference for all bases aligned to the reference sequence. |
| PF_HQ_ERROR_RATE | The fraction of bases that mismatch the reference in PF HQ aligned reads. |
| PF_INDEL_RATE | The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases. |
| MEAN_READ_LENGTH | The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads. |
| READS_ALIGNED_IN_PAIRS | The number of aligned reads whose mate pair was also aligned to the reference. |
| PCT_READS_ALIGNED_IN_PAIRS | The fraction of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED |
| PF_READS_IMPROPER_PAIRS | The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2). |
| PCT_PF_READS_IMPROPER_PAIRS | The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2). PF_READS_IMPROPER_PAIRS / PF_READS_ALIGNED |
| BAD_CYCLES | The number of instrument cycles in which 80% or more of base calls were no-calls. |
| STRAND_BALANCE | The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome. |
| PCT_CHIMERAS | The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes. |
| PCT_ADAPTER | The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read. |
BaseDistributionByCycleMetrics
| Field | Description |
|---|---|
| READ_END | |
| CYCLE | |
| PCT_A | |
| PCT_C | |
| PCT_G | |
| PCT_T | |
| PCT_N |
ClusteredCrosscheckMetric
A Metric class to hold the result of clustered crosschecking fingerprints. The same metric will be used for crosschecking Readgroups, libraries, samples, or files.
| Field | Description |
|---|---|
| CLUSTER | |
| CLUSTER_SIZE |
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
| Field | Description |
|---|---|
| TILE | The Tile that is described by this metric |
| X | The X coordinate of the read within the tile |
| Y | The Y coordinate of the read within the tile |
| NUM_N | The number of Ns found in this read |
| NUM_Q_GT_TWO | The number of Quality scores greater than 2 found in this read |
| CLASSIFICATION | The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.) |
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF. Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)
| Field | Description |
|---|---|
| TILE | The Tile that is described by this metric. Can be a string (like "All") to mean some marginal over tiles. * |
| READS | The total number of reads examined |
| PF_FAIL_READS | The number of non-PF reads in this tile. |
| PCT_PF_FAIL_READS | The fraction of PF_READS |
| PF_FAIL_EMPTY | The number of non-PF reads in this tile that are deemed empty. |
| PCT_PF_FAIL_EMPTY | The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads). |
| PF_FAIL_POLYCLONAL | The number of non-PF reads in this tile that are deemed multiclonal. |
| PCT_PF_FAIL_POLYCLONAL | The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads). |
| PF_FAIL_MISALIGNED | The number of non-PF reads in this tile that are deemed "misaligned". |
| PCT_PF_FAIL_MISALIGNED | The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads). |
| PF_FAIL_UNKNOWN | The number of non-PF reads in this tile that have not been classified. |
| PCT_PF_FAIL_UNKNOWN | The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads). |
CollectOxoGMetrics.CpcgMetrics
Metrics class for outputs.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | The name of the sample being assayed. |
| LIBRARY | The name of the library being assayed. |
| CONTEXT | The sequence context being reported on. |
| TOTAL_SITES | The total number of sites that had at least one base covering them. |
| TOTAL_BASES | The total number of basecalls observed at all sites. |
| REF_NONOXO_BASES | The number of reference alleles observed as C in read 1 and G in read 2. |
| REF_OXO_BASES | The number of reference alleles observed as G in read 1 and C in read 2. |
| REF_TOTAL_BASES | The total number of reference alleles observed |
| ALT_NONOXO_BASES | The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause |
| ALT_OXO_BASES | The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage. |
| OXIDATION_ERROR_RATE | The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES |
| OXIDATION_Q | -10 * log10(OXIDATION_ERROR_RATE) |
| C_REF_REF_BASES | The number of ref basecalls observed at sites where the genome reference == C. |
| G_REF_REF_BASES | The number of ref basecalls observed at sites where the genome reference == G. |
| C_REF_ALT_BASES | The number of alt (A/T) basecalls observed at sites where the genome reference == C. |
| G_REF_ALT_BASES | The number of alt (A/T) basecalls observed at sites where the genome reference == G. |
| C_REF_OXO_ERROR_RATE | The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. |
| C_REF_OXO_Q | C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. |
| G_REF_OXO_ERROR_RATE | The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. |
| G_REF_OXO_Q | G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. |
CollectQualityYieldMetrics.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM file
| Field | Description |
|---|---|
| TOTAL_READS | The total number of reads in the input file |
| PF_READS | The number of reads that are PF - pass filter |
| READ_LENGTH | The average read length of all the reads (will be fixed for a lane) |
| TOTAL_BASES | The total number of bases in all reads |
| PF_BASES | The total number of bases in all PF reads |
| Q20_BASES | The number of bases in all reads that achieve quality score 20 or higher |
| PF_Q20_BASES | The number of bases in PF reads that achieve quality score 20 or higher |
| Q30_BASES | The number of bases in all reads that achieve quality score 30 or higher |
| PF_Q30_BASES | The number of bases in PF reads that achieve quality score 30 or higher |
| Q20_EQUIVALENT_YIELD | The sum of quality scores of all bases divided by 20 |
| PF_Q20_EQUIVALENT_YIELD | The sum of quality scores of all bases in PF reads divided by 20 |
CollectRawWgsMetrics.RawWgsMetrics
| Field | Description |
|---|
CollectVariantCallingMetrics.VariantCallingDetailMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | The name of the sample being assayed |
| HET_HOMVAR_RATIO | (count of hets)/(count of homozygous non-ref) for this sample |
| PCT_GQ0_VARIANTS | The percentage of variants in a particular sample that have a GQ score of 0. |
| TOTAL_GQ0_VARIANTS | The total number of variants in a particular sample that have a GQ score of 0. |
| TOTAL_HET_DEPTH | total number of reads (from AD field) for passing bi-allelic SNP hets for this sample |
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
| Field | Description |
|---|---|
| TOTAL_SNPS | The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined |
| NUM_IN_DB_SNP | The number of passing bi-allelic SNPs found in dbSNP |
| NOVEL_SNPS | The number of passing bi-allelic SNPS called that were not found in dbSNP |
| FILTERED_SNPS | The number of SNPs that are filtered |
| PCT_DBSNP | The fraction of passing bi-allelic SNPs in dbSNP |
| DBSNP_TITV | The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites |
| NOVEL_TITV | The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites |
| TOTAL_INDELS | The number of passing indel calls that were examined |
| NOVEL_INDELS | The number of passing indels called that were not found in dbSNP |
| FILTERED_INDELS | The number of indels that are filtered |
| PCT_DBSNP_INDELS | The fraction of passing indels in dbSNP |
| NUM_IN_DB_SNP_INDELS | The number of passing indels found in dbSNP |
| DBSNP_INS_DEL_RATIO | The Insertion/Deletion ratio of the indel calls made at dbSNP sites |
| NOVEL_INS_DEL_RATIO | The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites |
| TOTAL_MULTIALLELIC_SNPS | The number of passing multi-allelic SNP calls that were examined |
| NUM_IN_DB_SNP_MULTIALLELIC | The number of passing multi-allelic SNPs found in dbSNP |
| TOTAL_COMPLEX_INDELS | The number of passing complex indel calls that were examined |
| NUM_IN_DB_SNP_COMPLEX_INDELS | The number of passing complex indels found in dbSNP |
| SNP_REFERENCE_BIAS | The rate at which reference bases are observed at ref/alt heterozygous SNP sites. |
| NUM_SINGLETONS | For summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample. |
CollectWgsMetrics.WgsMetrics
Metrics for evaluating the performance of whole genome sequencing experiments.
| Field | Description |
|---|---|
| GENOME_TERRITORY | The number of non-N bases in the genome reference over which coverage will be evaluated. |
| MEAN_COVERAGE | The mean coverage in bases of the genome territory, after all filters are applied. |
| SD_COVERAGE | The standard deviation of coverage of the genome after all filters are applied. |
| MEDIAN_COVERAGE | The median coverage in bases of the genome territory, after all filters are applied. |
| MAD_COVERAGE | The median absolute deviation of coverage of the genome after all filters are applied. |
| PCT_EXC_MAPQ | The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20). |
| PCT_EXC_DUPE | The fraction of aligned bases that were filtered out because they were in reads marked as duplicates. |
| PCT_EXC_UNPAIRED | The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair. |
| PCT_EXC_BASEQ | The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20). |
| PCT_EXC_OVERLAP | The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. |
| PCT_EXC_CAPPED | The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x). |
| PCT_EXC_TOTAL | The total fraction of aligned bases excluded due to all filters. |
| PCT_1X | The fraction of bases that attained at least 1X sequence coverage in post-filtering bases. |
| PCT_5X | The fraction of bases that attained at least 5X sequence coverage in post-filtering bases. |
| PCT_10X | The fraction of bases that attained at least 10X sequence coverage in post-filtering bases. |
| PCT_15X | The fraction of bases that attained at least 15X sequence coverage in post-filtering bases. |
| PCT_20X | The fraction of bases that attained at least 20X sequence coverage in post-filtering bases. |
| PCT_25X | The fraction of bases that attained at least 25X sequence coverage in post-filtering bases. |
| PCT_30X | The fraction of bases that attained at least 30X sequence coverage in post-filtering bases. |
| PCT_40X | The fraction of bases that attained at least 40X sequence coverage in post-filtering bases. |
| PCT_50X | The fraction of bases that attained at least 50X sequence coverage in post-filtering bases. |
| PCT_60X | The fraction of bases that attained at least 60X sequence coverage in post-filtering bases. |
| PCT_70X | The fraction of bases that attained at least 70X sequence coverage in post-filtering bases. |
| PCT_80X | The fraction of bases that attained at least 80X sequence coverage in post-filtering bases. |
| PCT_90X | The fraction of bases that attained at least 90X sequence coverage in post-filtering bases. |
| PCT_100X | The fraction of bases that attained at least 100X sequence coverage in post-filtering bases. |
| HET_SNP_SENSITIVITY | The theoretical HET SNP sensitivity. |
| HET_SNP_Q | The Phred Scaled Q Score of the theoretical HET SNP sensitivity. |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
Metrics for evaluating the performance of whole genome sequencing experiments.
| Field | Description |
|---|---|
| CATEGORY | One of either WHOLE_GENOME or NON_ZERO_REGIONS |
CrosscheckMetric
A class to hold the result of crosschecking fingerprints. The same metric will be used for crosschecking Readgroups, libraries, samples, or files.
| Field | Description |
|---|---|
| LEFT_GROUP_VALUE | |
| RIGHT_GROUP_VALUE | |
| RESULT | |
| DATA_TYPE | |
| LOD_SCORE | |
| LOD_SCORE_TUMOR_NORMAL | |
| LOD_SCORE_NORMAL_TUMOR | |
| LEFT_RUN_BARCODE | |
| LEFT_LANE | |
| LEFT_MOLECULAR_BARCODE_SEQUENCE | |
| LEFT_LIBRARY | |
| LEFT_SAMPLE | |
| LEFT_FILE | |
| RIGHT_RUN_BARCODE | |
| RIGHT_LANE | |
| RIGHT_MOLECULAR_BARCODE_SEQUENCE | |
| RIGHT_LIBRARY | |
| RIGHT_SAMPLE | |
| RIGHT_FILE |
DuplicationMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
| Field | Description |
|---|---|
| LIBRARY | The library on which the duplicate marking was performed. |
| UNPAIRED_READS_EXAMINED | The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate. |
| READ_PAIRS_EXAMINED | The number of mapped read pairs examined. (Primary, non-supplemental) |
| SECONDARY_OR_SUPPLEMENTARY_RDS | The number of reads that were either secondary or supplementary |
| UNMAPPED_READS | The total number of unmapped reads examined. (Primary, non-supplemental) |
| UNPAIRED_READ_DUPLICATES | The number of fragments that were marked as duplicates. |
| READ_PAIR_DUPLICATES | The number of read pairs that were marked as duplicates. |
| READ_PAIR_OPTICAL_DUPLICATES | The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source. |
| PERCENT_DUPLICATION | The fraction of mapped sequence that is marked as duplicate. |
| ESTIMATED_LIBRARY_SIZE | The estimated number of unique molecules in the library based on PE duplication. |
ErrorSummaryMetrics
Summary metrics produced by {@link CollectSequencingArtifactMetrics} as a roll up of the context-specific error rates, to provide global error rates per type of base substitution. Errors are normalized to the lexically lower reference base and summarized together. E.g. G>T is converted to C>A and merged with data from C>A for reporting.
| Field | Description |
|---|---|
| REF_BASE | The reference base (or it's complement). |
| ALT_BASE | The alternative base (or it's complement). |
| SUBSTITUTION | A single string representing the substition from REF_BASE to ALT_BASE for convenience. |
| REF_COUNT | The number of reference bases observed. |
| ALT_COUNT | The number of alt bases observed. |
| SUBSTITUTION_RATE | The rate of the substitution in question. |
ExtractIlluminaBarcodes.BarcodeMetric
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
| Field | Description |
|---|---|
| BARCODE | The barcode (from the set of expected barcodes) for which the following metrics apply. Note that the "symbolic" barcode of NNNNNN is used to report metrics for all reads that do not match a barcode. |
| BARCODE_WITHOUT_DELIMITER | |
| BARCODE_NAME | The barcode name. |
| LIBRARY_NAME | The name of the library |
| READS | The total number of reads matching the barcode. |
| PF_READS | The number of PF reads matching this barcode (always less than or equal to READS). |
| PERFECT_MATCHES | The number of all reads matching this barcode that matched with 0 errors or no-calls. |
| PF_PERFECT_MATCHES | The number of PF reads matching this barcode that matched with 0 errors or no-calls. |
| ONE_MISMATCH_MATCHES | The number of all reads matching this barcode that matched with 1 error or no-call. |
| PF_ONE_MISMATCH_MATCHES | The number of PF reads matching this barcode that matched with 1 error or no-call. |
| PCT_MATCHES | The fraction of all reads in the lane that matched to this barcode. |
| RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT | The rate of all reads matching this barcode to all reads matching the most prevelant barcode. For the most prevelant barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes. |
| PF_PCT_MATCHES | The fraction of PF reads in the lane that matched to this barcode. |
| PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT | The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode. For the most prevelant barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation of PF reads between barcodes. |
| PF_NORMALIZED_MATCHES | The "normalized" matches to each barcode. This is calculated as the number of pf reads matching this barcode over the sum of all pf reads matching any barcode (excluding orphans). If all barcodes are represented equally this will be 1. |
FingerprintingDetailMetrics
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
| Field | Description |
|---|---|
| READ_GROUP | The sequencing read group from which sequence data was fingerprinted. |
| SAMPLE | The name of the sample who's genotypes the sequence data was compared to. |
| SNP | The name of a representative SNP within the haplotype that was compared. Will usually be the exact SNP that was genotyped externally. |
| SNP_ALLELES | The possible alleles for the SNP. |
| CHROM | The chromosome on which the SNP resides. |
| POSITION | The position of the SNP on the chromosome. |
| EXPECTED_GENOTYPE | The expected genotype of the sample at the SNP locus. |
| OBSERVED_GENOTYPE | The most likely genotype given the observed evidence at the SNP locus in the sequencing data. |
| LOD | The LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data. |
| OBS_A | The number of observations of the first, or A, allele of the SNP in the sequencing data. |
| OBS_B | The number of observations of the second, or B, allele of the SNP in the sequencing data. |
FingerprintingSummaryMetrics
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs. a set of known genotypes for the expected sample.
| Field | Description |
|---|---|
| READ_GROUP | The read group from which sequence data was drawn for comparison. |
| SAMPLE | The sample whose known genotypes the sequence data was compared to. |
| LL_EXPECTED_SAMPLE | The Log Likelihood of the sequence data given the expected sample's genotypes. |
| LL_RANDOM_SAMPLE | The Log Likelihood of the sequence data given a random sample from the human population. |
| LOD_EXPECTED_SAMPLE | The LOD for Expected Sample vs. Random Sample. A positive LOD indicates that the sequence data is more likely to come from the expected sample vs. a random sample from the population, by LOD logs. I.e. a value of 6 indicates that the sequence data is 1,000,000 more likely to come from the expected sample than from a random sample. A negative LOD indicates the reverse - that the sequence data is more likely to come from a random sample than from the expected sample. |
| HAPLOTYPES_WITH_GENOTYPES | The number of haplotypes that had expected genotypes to compare to. |
| HAPLOTYPES_CONFIDENTLY_CHECKED | The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype. Note: all haplotypes with sequence coverage contribute to the LOD score, even if they cannot be "confidently checked" individually. |
| HAPLOTYPES_CONFIDENTLY_MATCHING | The subset of confidently checked haplotypes that match the expected genotypes. |
| HET_AS_HOM | num of hets, observed as homs with LOD > threshold |
| HOM_AS_HET | num of homs, observed as hets with LOD > threshold |
| HOM_AS_OTHER_HOM | num of homs, observed as other homs with LOD > threshold |
GcBiasDetailMetrics
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
| Field | Description |
|---|---|
| ACCUMULATION_LEVEL | |
| READS_USED | This option is used to mark including or excluding duplicates. |
| GC | The G+C content of the reference sequence represented by this bin. Values are from 0% to 100% |
| WINDOWS | The number of windows on the reference genome that have this G+C content. |
| READ_STARTS | The number of reads whose start position is at the start of a window of this GC. |
| MEAN_BASE_QUALITY | The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC. |
| NORMALIZED_COVERAGE | The ratio of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average). |
| ERROR_BAR_WIDTH | The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85. |
GcBiasMetrics
| Field | Description |
|---|---|
| DETAILS | |
| SUMMARY |
GcBiasSummaryMetrics
High level metrics that capture how biased the coverage in a certain lane is.
| Field | Description |
|---|---|
| ACCUMULATION_LEVEL | |
| READS_USED | This option is used to mark including or excluding duplicates. |
| WINDOW_SIZE | The window size on the genome used to calculate the GC of the sequence. |
| TOTAL_CLUSTERS | The total number of clusters that were seen in the gc bias calculation. |
| ALIGNED_READS | The total number of aligned reads used to compute the gc bias metrics. |
| AT_DROPOUT | Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50]. |
| GC_DROPOUT | Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100]. |
| GC_NC_0_19 | Normalized coverage over quintile of GC content ranging from 0 - 19. |
| GC_NC_20_39 | Normalized coverage over each quintile of GC content ranging from 20 - 39. |
| GC_NC_40_59 | Normalized coverage over each quintile of GC content ranging from 40 - 59. |
| GC_NC_60_79 | Normalized coverage over each quintile of GC content ranging from 60 - 79. |
| GC_NC_80_100 | Normalized coverage over each quintile of GC content ranging from 80 - 100. |
GenotypeConcordanceContingencyMetrics
Class that holds metrics about the Genotype Concordance contingency tables.
| Field | Description |
|---|---|
| VARIANT_TYPE | The type of the event (i.e. either SNP or INDEL) |
| TRUTH_SAMPLE | The name of the 'truth' sample |
| CALL_SAMPLE | The name of the 'call' sample |
| TP_COUNT | The TP (true positive) count across all variants |
| TN_COUNT | The TN (true negative) count across all variants |
| FP_COUNT | The FP (false positive) count across all variants |
| FN_COUNT | The FN (false negative) count across all variants |
| EMPTY_COUNT | The empty (no contingency info) count across all variants |
GenotypeConcordanceDetailMetrics
Class that holds detail metrics about Genotype Concordance
| Field | Description |
|---|---|
| VARIANT_TYPE | The type of the event (i.e. either SNP or INDEL) |
| TRUTH_SAMPLE | The name of the 'truth' sample |
| CALL_SAMPLE | The name of the 'call' sample |
| TRUTH_STATE | The state of the 'truth' sample (i.e. HOM_REF, HET_REF_VAR1, HET_VAR1_VAR2...) |
| CALL_STATE | The state of the 'call' sample (i.e. HOM_REF, HET_REF_VAR1...) |
| COUNT | The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs |
| CONTINGENCY_VALUES | The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference. In general, we are comparing two sets of alleles. Therefore, we can have zero or more contingency table values represented in one comparison. For example, if the truthset is a heterozygous call with both alleles non-reference (HET_VAR1_VAR2), and the callset is a heterozygous call with both alleles non-reference with one of the alternate alleles matching an alternate allele in the callset, we would have a true positive, false positive, and false negative. The true positive is from the matching alternate alleles, the false positive is the alternate allele found in the callset but not found in the truthset, and the false negative is the alternate in the truthset not found in the callset. We also include a true negative in cases where the reference allele is found in both the truthset and callset. |
GenotypeConcordanceSummaryMetrics
Class that holds summary metrics about Genotype Concordance
| Field | Description |
|---|---|
| VARIANT_TYPE | The type of the event (i.e. either SNP or INDEL) |
| TRUTH_SAMPLE | The name of the 'truth' sample |
| CALL_SAMPLE | The name of the 'call' sample |
| HET_SENSITIVITY | The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN)) |
| HET_PPV | The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP)) |
| HET_SPECIFICITY | The specificity for all heterozygous variants cannot be calculated |
| HOMVAR_SENSITIVITY | The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN)) |
| HOMVAR_PPV | The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP)) |
| HOMVAR_SPECIFICITY | The specificity for all homozygous variants cannot be calculated. |
| VAR_SENSITIVITY | The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN)) |
| VAR_PPV | The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP)) |
| VAR_SPECIFICITY | The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN)) |
| GENOTYPE_CONCORDANCE | The genotype concordance for all possible states. Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made |
| NON_REF_GENOTYPE_CONCORDANCE | The non-ref genotype concordance, ie for all var states only. Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made |
HsMetrics
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments. The metrics in this class fall broadly into three categories:
- Basic sequencing metrics that are either generated as a baseline against which to evaluate other metrics or because they are used in the calculation of other metrics. This includes things like the genome size, the number of reads, the number of aligned reads etc.
- Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle of paired-end reads are all counted).
- Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases reaching various coverage levels, and the percentage of bases excluded by various filters. These metrics are computed using the strictest subset of the data, after all filters have been applied.
| Field | Description |
|---|---|
| BAIT_SET | The name of the bait set used in the hybrid selection. |
| GENOME_SIZE | The number of bases in the reference genome used for alignment. |
| BAIT_TERRITORY | The number of bases which are localized to one or more baits. |
| TARGET_TERRITORY | The unique number of target bases in the experiment, where the target sequence is usually exons etc. |
| BAIT_DESIGN_EFFICIENCY | The ratio of TARGET_TERRITORY/BAIT_TERRITORY. A value of 1 indicates a perfect design efficiency, while a valud of 0.5 indicates that half of bases within the bait region are not within the target region. |
| TOTAL_READS | The total number of reads in the SAM or BAM file examined. |
| PF_READS | The total number of reads that pass the vendor's filter. |
| PF_UNIQUE_READS | The number of PF reads that are not marked as duplicates. |
| PCT_PF_READS | The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS. |
| PCT_PF_UQ_READS | The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS. |
| PF_UQ_READS_ALIGNED | The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0. |
| PCT_PF_UQ_READS_ALIGNED | The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads. |
| PF_BASES_ALIGNED | The number of PF unique bases that are aligned to the reference genome with mapping scores > 0. |
| PF_UQ_BASES_ALIGNED | The number of bases in the PF_UQ_READS_ALIGNED reads. Accounts for clipping and gaps. |
| ON_BAIT_BASES | The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome. |
| NEAR_BAIT_BASES | The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se. |
| OFF_BAIT_BASES | The number of PF_BASES_ALIGNED that are mapped away from any baited region. |
| ON_TARGET_BASES | The number of PF_BASES_ALIGNED that are mapped to a targeted region of the genome. |
| PCT_SELECTED_BASES | The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED. |
| PCT_OFF_BAIT | The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED. |
| ON_BAIT_VS_SELECTED | The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES). |
| MEAN_BAIT_COVERAGE | The mean coverage of all baits in the experiment. |
| MEAN_TARGET_COVERAGE | The mean coverage of a target region. |
| MEDIAN_TARGET_COVERAGE | The median coverage of a target region. |
| MAX_TARGET_COVERAGE | The maximum coverage of reads that mapped to target regions of an experiment. |
| PCT_USABLE_BASES_ON_BAIT | The number of aligned, de-duped, on-bait bases out of the PF bases available. |
| PCT_USABLE_BASES_ON_TARGET | The number of aligned, de-duped, on-target bases out of all of the PF bases available. |
| FOLD_ENRICHMENT | The fold by which the baited region has been amplified above genomic background. |
| ZERO_CVG_TARGETS_PCT | The fraction of targets that did not reach coverage=1 over any base. |
| PCT_EXC_DUPE | The fraction of aligned bases that were filtered out because they were in reads marked as duplicates. |
| PCT_EXC_MAPQ | The fraction of aligned bases that were filtered out because they were in reads with low mapping quality. |
| PCT_EXC_BASEQ | The fraction of aligned bases that were filtered out because they were of low base quality. |
| PCT_EXC_OVERLAP | The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. |
| PCT_EXC_OFF_TARGET | The fraction of aligned bases that were filtered out because they did not align over a target base. |
| FOLD_80_BASE_PENALTY | The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets. |
| PCT_TARGET_BASES_1X | The fraction of all target bases achieving 1X or greater coverage. |
| PCT_TARGET_BASES_2X | The fraction of all target bases achieving 2X or greater coverage. |
| PCT_TARGET_BASES_10X | The fraction of all target bases achieving 10X or greater coverage. |
| PCT_TARGET_BASES_20X | The fraction of all target bases achieving 20X or greater coverage. |
| PCT_TARGET_BASES_30X | The fraction of all target bases achieving 30X or greater coverage. |
| PCT_TARGET_BASES_40X | The fraction of all target bases achieving 40X or greater coverage. |
| PCT_TARGET_BASES_50X | The fraction of all target bases achieving 50X or greater coverage. |
| PCT_TARGET_BASES_100X | The fraction of all target bases achieving 100X or greater coverage. |
| HS_LIBRARY_SIZE | The estimated number of unique molecules in the selected part of the library. |
| HS_PENALTY_10X | The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X. |
| HS_PENALTY_20X | The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X. |
| HS_PENALTY_30X | The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X. |
| HS_PENALTY_40X | The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X. |
| HS_PENALTY_50X | The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X. |
| HS_PENALTY_100X | The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X. |
| AT_DROPOUT | A measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC<=50% regions mapped elsewhere. |
| GC_DROPOUT | A measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC>=50% regions mapped elsewhere. |
| HET_SNP_SENSITIVITY | The theoretical HET SNP sensitivity. |
| HET_SNP_Q | The Phred Scaled Q Score of the theoretical HET SNP sensitivity. |
IlluminaBasecallingMetrics
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis. Averages and means are taken over all tiles.
| Field | Description |
|---|---|
| LANE | The lane for which the metrics were calculated. |
| MOLECULAR_BARCODE_SEQUENCE_1 | The barcode sequence for which the metrics were calculated. |
| MOLECULAR_BARCODE_NAME | The barcode name for which the metrics were calculated. |
| TOTAL_BASES | The total number of bases assigned to the index. |
| PF_BASES | The total number of passing-filter bases assigned to the index. |
| TOTAL_READS | The total number of reads assigned to the index. |
| PF_READS | The total number of passing-filter reads assigned to the index. |
| TOTAL_CLUSTERS | The total number of clusters assigned to the index. |
| PF_CLUSTERS | The total number of PF clusters assigned to the index. |
| MEAN_CLUSTERS_PER_TILE | The mean number of clusters per tile. |
| SD_CLUSTERS_PER_TILE | The standard deviation of clusters per tile. |
| MEAN_PCT_PF_CLUSTERS_PER_TILE | The mean percentage of pf clusters per tile. |
| SD_PCT_PF_CLUSTERS_PER_TILE | The standard deviation in percentage of pf clusters per tile. |
| MEAN_PF_CLUSTERS_PER_TILE | The mean number of pf clusters per tile. |
| SD_PF_CLUSTERS_PER_TILE | The standard deviation in number of pf clusters per tile. |
IlluminaLaneMetrics
Embodies characteristics that describe a lane.
| Field | Description |
|---|---|
| CLUSTER_DENSITY | The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2]. |
| LANE | This lane's number. |
IlluminaPhasingMetrics
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair.
| Field | Description |
|---|---|
| LANE | Illumina flowcell lane number |
| TYPE_NAME | Defines an Illumina template read number (first or second) |
| PHASING_APPLIED | Median phasing value across all tiles in a lane, applied to the first and second template reads |
| PREPHASING_APPLIED | Median pre-phasing value across all tiles in a lane, applied to the first and second template reads |
IndependentReplicateMetric
A class to store information relevant for biological rate estimation
| Field | Description |
|---|---|
| nSites | |
| nThreeAllelesSites | |
| nTotalReads | |
| nDuplicateSets | |
| nExactlyTriple | |
| nExactlyDouble | |
| nReadsInBigSets | |
| nDifferentAllelesBiDups | |
| nReferenceAllelesBiDups | |
| nAlternateAllelesBiDups | |
| nDifferentAllelesTriDups | |
| nMismatchingAllelesBiDups | |
| nReferenceAllelesTriDups | |
| nAlternateAllelesTriDups | |
| nMismatchingAllelesTriDups | |
| nReferenceReads | |
| nAlternateReads | |
| nMismatchingUMIsInDiffBiDups | |
| nMatchingUMIsInDiffBiDups | |
| nMismatchingUMIsInSameBiDups | |
| nMatchingUMIsInSameBiDups | |
| nMismatchingUMIsInCoOrientedBiDups | |
| nMismatchingUMIsInContraOrientedBiDups | |
| nBadBarcodes | |
| nGoodBarcodes | |
| biSiteHeterogeneityRate | |
| triSiteHeterogeneityRate | |
| biSiteHomogeneityRate | |
| triSiteHomogeneityRate | |
| independentReplicationRateFromBiDups | |
| independentReplicationRateFromTriDups | |
| pSameUmiInIndependentBiDup | |
| pSameAlleleWhenMismatchingUmi | |
| independentReplicationRateFromUmi | |
| replicationRateFromReplicateSets |
InsertSizeMetrics
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics". In addition the insert size distribution is plotted to a file with the extension ".insert_size_Histogram.pdf".
| Field | Description |
|---|---|
| MEDIAN_INSERT_SIZE | The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome. |
| MEDIAN_ABSOLUTE_DEVIATION | The median absolute deviation of the distribution. If the distribution is essentially normal then the standard deviation can be estimated as ~1.4826 * MAD. |
| MIN_INSERT_SIZE | The minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual. |
| MAX_INSERT_SIZE | The maximum measure insert size by alignment. This is usually very high representing either an artifact or possibly the presence of a structural re-arrangement. |
| MEAN_INSERT_SIZE | The mean insert size of the "core" of the distribution. Artefactual outliers in the distribution often cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed to a "core" distribution of +/- N median absolute deviations around the median insert size. By default N=10, but this is configurable. |
| STANDARD_DEVIATION | Standard deviation of insert sizes over the "core" of the distribution. |
| READ_PAIRS | The total number of read pairs that were examined in the entire distribution. |
| PAIR_ORIENTATION | The pair orientation of the reads in this data category. |
| WIDTH_OF_10_PERCENT | The "width" of the bins, centered around the median, that encompass 10% of all read pairs. |
| WIDTH_OF_20_PERCENT | The "width" of the bins, centered around the median, that encompass 20% of all read pairs. |
| WIDTH_OF_30_PERCENT | The "width" of the bins, centered around the median, that encompass 30% of all read pairs. |
| WIDTH_OF_40_PERCENT | The "width" of the bins, centered around the median, that encompass 40% of all read pairs. |
| WIDTH_OF_50_PERCENT | The "width" of the bins, centered around the median, that encompass 50% of all read pairs. |
| WIDTH_OF_60_PERCENT | The "width" of the bins, centered around the median, that encompass 60% of all read pairs. |
| WIDTH_OF_70_PERCENT | The "width" of the bins, centered around the median, that encompass 70% of all read pairs. This metric divided by 2 should approximate the standard deviation when the insert size distribution is a normal distribution. |
| WIDTH_OF_80_PERCENT | The "width" of the bins, centered around the median, that encompass 80% of all read pairs. |
| WIDTH_OF_90_PERCENT | The "width" of the bins, centered around the median, that encompass 90% of all read pairs. |
| WIDTH_OF_99_PERCENT | The "width" of the bins, centered around the median, that encompass 100% of all read pairs. |
JumpingLibraryMetrics
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
| Field | Description |
|---|---|
| JUMP_PAIRS | The number of outward-facing pairs in the SAM file |
| JUMP_DUPLICATE_PAIRS | The number of outward-facing pairs that are duplicates |
| JUMP_DUPLICATE_PCT | The fraction of outward-facing pairs that are marked as duplicates |
| JUMP_LIBRARY_SIZE | The estimated library size for outward-facing pairs |
| JUMP_MEAN_INSERT_SIZE | The mean insert size for outward-facing pairs |
| JUMP_STDEV_INSERT_SIZE | The standard deviation on the insert size for outward-facing pairs |
| NONJUMP_PAIRS | The number of inward-facing pairs in the SAM file |
| NONJUMP_DUPLICATE_PAIRS | The number of inward-facing pais that are duplicates |
| NONJUMP_DUPLICATE_PCT | The fraction of inward-facing pairs that are marked as duplicates |
| NONJUMP_LIBRARY_SIZE | The estimated library size for inward-facing pairs |
| NONJUMP_MEAN_INSERT_SIZE | The mean insert size for inward-facing pairs |
| NONJUMP_STDEV_INSERT_SIZE | The standard deviation on the insert size for inward-facing pairs |
| CHIMERIC_PAIRS | The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs. |
| FRAGMENTS | The number of fragments in the SAM file |
| PCT_JUMPS | The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
| PCT_NONJUMPS | The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
| PCT_CHIMERAS | The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
MendelianViolationMetrics
Describes the type and number of mendelian violations found within a Trio.
| Field | Description |
|---|---|
| FAMILY_ID | The family ID assigned to the trio for which these metrics are calculated. |
| MOTHER | The ID of the mother within the trio. |
| FATHER | The ID of the father within the trio. |
| OFFSPRING | The ID of the offspring within the trio. |
| OFFSPRING_SEX | The sex of the offspring. |
| NUM_VARIANT_SITES | The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant. |
| NUM_DIPLOID_DENOVO | The number of diploid sites at which a potential de-novo mutation was observed (i.e. both parents are hom-ref, offspring is not hom-ref. |
| NUM_HOMVAR_HOMVAR_HET | The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous. |
| NUM_HOMREF_HOMVAR_HOM | The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous. |
| NUM_HOM_HET_HOM | The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote. |
| NUM_HAPLOID_DENOVO | The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference. |
| NUM_HAPLOID_OTHER | The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent. |
| NUM_OTHER | The number of otherwise unclassified events. |
| TOTAL_MENDELIAN_VIOLATIONS | The total of all mendelian violations observed. |
MergeableMetricBase
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated. It also provides an interface for calculating derived fields (and an annotation that informs that said fields are derived). Finally, it also allows for an annotation that suggests that a field will be used as an ID and thus merging will simply require that these fields are equal. merge-by-adding is only enabled for the following types: int, Integer, float, Float, double, Double, short, Short, long, Long, byte, Byte. Overflow will be detected (for the short, and byte types) and an exception thrown.
| Field | Description |
|---|
MultilevelMetrics
| Field | Description |
|---|---|
| SAMPLE | The sample to which these metrics apply. If null, it means they apply to all reads in the file. |
| LIBRARY | The library to which these metrics apply. If null, it means that the metrics were accumulated at the sample level. |
| READ_GROUP | The read group to which these metrics apply. If null, it means that the metrics were accumulated at the library or sample level. |
RnaSeqMetrics
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
| Field | Description |
|---|---|
| PF_BASES | The total number of PF bases including non-aligned reads. |
| PF_ALIGNED_BASES | The total number of aligned PF bases. Non-primary alignments are not counted. Bases in aligned reads that do not correspond to reference (e.g. soft clips, insertions) are not counted. |
| RIBOSOMAL_BASES | Number of bases in primary alignments that align to ribosomal sequence. |
| CODING_BASES | Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence. |
| UTR_BASES | Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base. |
| INTRONIC_BASES | Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base. |
| INTERGENIC_BASES | Number of bases in primary alignments that do not align to any gene. |
| IGNORED_READS | Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE. These are not counted in PF_ALIGNED_BASES, CORRECT_STRAND_READS, INCORRECT_STRAND_READS, or any of the base-counting metrics. These reads are counted in PF_BASES. |
| CORRECT_STRAND_READS | Number of aligned reads that are mapped to the correct strand. 0 if library is not strand-specific. |
| INCORRECT_STRAND_READS | Number of aligned reads that are mapped to the incorrect strand. 0 if library is not strand-specific. |
| NUM_R1_TRANSCRIPT_STRAND_READS | The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand. |
| NUM_R2_TRANSCRIPT_STRAND_READS | The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand. |
| NUM_UNEXPLAINED_READS | The fraction of reads for which the transcription strand model could not be inferred. |
| PCT_R1_TRANSCRIPT_STRAND_READS | The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand. For unpaired reads, it is the fraction of reads that are on the transcription strand (out of all the reads). |
| PCT_R2_TRANSCRIPT_STRAND_READS | The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand. For unpaired reads, it is the fraction of reads that are on opposite strand than that of the the transcription strand (out of all the reads). |
| PCT_RIBOSOMAL_BASES | Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES |
| PCT_CODING_BASES | Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES |
| PCT_UTR_BASES | Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES |
| PCT_INTRONIC_BASES | Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES |
| PCT_INTERGENIC_BASES | Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES |
| PCT_MRNA_BASES | Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES |
| PCT_USABLE_BASES | The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES. |
| PCT_CORRECT_STRAND_READS | Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS). 0 if library is not strand-specific. |
| MEDIAN_CV_COVERAGE | The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts. Ideal value = 0. |
| MEDIAN_5PRIME_BIAS | The median 5 prime bias of the 1000 most highly expressed transcripts. The 5 prime bias is calculated per transcript as: mean coverage of the 5 prime-most 100 bases divided by the mean coverage of the whole transcript. |
| MEDIAN_3PRIME_BIAS | The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most 100 bases divided by the mean coverage of the whole transcript. |
| MEDIAN_5PRIME_TO_3PRIME_BIAS | The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts. |
RrbsCpgDetailMetrics
Holds information about CpG sites encountered for RRBS processing QC
| Field | Description |
|---|---|
| SEQUENCE_NAME | Sequence the CpG is seen in |
| POSITION | Position within the sequence of the CpG site |
| TOTAL_SITES | Number of times this CpG site was encountered |
| CONVERTED_SITES | Number of times this CpG site was converted (TG for + strand, CA for - strand) |
| PCT_CONVERTED | CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction) |
RrbsSummaryMetrics
Holds summary statistics from RRBS processing QC
| Field | Description |
|---|---|
| READS_ALIGNED | Number of mapped reads processed |
| NON_CPG_BASES | Number of times a non-CpG cytosine was encountered |
| NON_CPG_CONVERTED_BASES | Number of times a non-CpG cytosine was converted (C->T for +, G->A for -) |
| PCT_NON_CPG_BASES_CONVERTED | NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction) |
| CPG_BASES_SEEN | Number of CpG sites encountered |
| CPG_BASES_CONVERTED | Number of CpG sites that were converted (TG for +, CA for -) |
| PCT_CPG_BASES_CONVERTED | CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction) |
| MEAN_CPG_COVERAGE | Mean coverage of CpG sites |
| MEDIAN_CPG_COVERAGE | Median coverage of CpG sites |
| READS_WITH_NO_CPG | Number of reads discarded for having no CpG sites |
| READS_IGNORED_SHORT | Number of reads discarded due to being too short |
| READS_IGNORED_MISMATCHES | Number of reads discarded for exceeding the mismatch threshold |
SequencingArtifactMetrics.BaitBiasDetailMetrics
Bait bias artifacts broken down by context.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | |
| LIBRARY | The name of the library being assayed. |
| REF_BASE | The (upper-case) original base on the reference strand. |
| ALT_BASE | The (upper-case) alternative base that is called as a result of DNA damage. |
| CONTEXT | The sequence context to which the analysis is constrained. |
| FWD_CXT_REF_BASES | The number of REF_BASE:REF_BASE alignments at sites with the given reference context. |
| FWD_CXT_ALT_BASES | The number of REF_BASE:ALT_BASE alignments at sites with the given reference context. |
| REV_CXT_REF_BASES | The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context. |
| REV_CXT_ALT_BASES | The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context. |
| FWD_ERROR_RATE | The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)). |
| REV_ERROR_RATE | The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)). |
| ERROR_RATE | The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE). |
| QSCORE | The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE). |
SequencingArtifactMetrics.BaitBiasSummaryMetrics
Summary analysis of a single bait bias artifact, also known as a reference bias artifact. These artifacts occur during or after the target selection step, and correlate with substitution rates that are "biased", or higher for sites having one base on the reference/positive strand relative to sites having the complementary base on that strand. For example, a G>T artifact during the target selection step might result in a higher G>T / C>A substitution rate at sites with a G on the positive strand (and C on the negative), relative to sites with the flip (C positive / G negative). This is known as the "G-Ref" artifact.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | The name of the sample being assayed. |
| LIBRARY | The name of the library being assayed. |
| REF_BASE | The (upper-case) original base on the reference strand. |
| ALT_BASE | The (upper-case) alternative base that is called as a result of DNA damage. |
| TOTAL_QSCORE | The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant. |
| WORST_CXT | The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact. |
| WORST_CXT_QSCORE | The Q-score for the worst context. |
| WORST_PRE_CXT | The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score. |
| WORST_PRE_CXT_QSCORE | The Q-score for the worst pre-context. |
| WORST_POST_CXT | The post-context (reference bases trailing after the locus of interest) with the lowest Q-score. |
| WORST_POST_CXT_QSCORE | The Q-score for the worst post-context. |
| ARTIFACT_NAME | A "nickname" of this artifact, if it is a known error mode. |
SequencingArtifactMetrics.PreAdapterDetailMetrics
Pre-adapter artifacts broken down by context.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | The name of the sample being assayed. |
| LIBRARY | The name of the library being assayed. |
| REF_BASE | The (upper-case) original base on the reference strand. |
| ALT_BASE | The (upper-case) alternative base that is called as a result of DNA damage. |
| CONTEXT | The sequence context to which the analysis is constrained. |
| PRO_REF_BASES | The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact. |
| PRO_ALT_BASES | The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact. |
| CON_REF_BASES | The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact. |
| CON_ALT_BASES | The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact. |
| ERROR_RATE | The estimated error rate due to this artifact. Calculated as max(1e-10, (PRO_ALT_BASES - CON_ALT_BASES) / (PRO_ALT_BASES + PRO_REF_BASES + CON_ALT_BASES + CON_REF_BASES)). |
| QSCORE | The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE). |
SequencingArtifactMetrics.PreAdapterSummaryMetrics
Summary analysis of a single pre-adapter artifact. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number / orientation in a specific way. For example, the well-known "Oxo-G" artifact occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be: 1. a true mutation 2. an OxoG artifact 3. some other kind of artifact On average, we assume that 1 and 3 will not display this read number / orientation bias, so their contributions will cancel out in the calculation.
| Field | Description |
|---|---|
| SAMPLE_ALIAS | The name of the sample being assayed. |
| LIBRARY | The name of the library being assayed. |
| REF_BASE | The (upper-case) original base on the reference strand. |
| ALT_BASE | The (upper-case) alternative base that is called as a result of DNA damage. |
| TOTAL_QSCORE | The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant. |
| WORST_CXT | The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact. |
| WORST_CXT_QSCORE | The Q-score for the worst context. |
| WORST_PRE_CXT | The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score. |
| WORST_PRE_CXT_QSCORE | The Q-score for the worst pre-context. |
| WORST_POST_CXT | The post-context (reference bases trailing after the locus of interest) with the lowest Q-score. |
| WORST_POST_CXT_QSCORE | The Q-score for the worst post-context. |
| ARTIFACT_NAME | A "nickname" of this artifact, if it is a known error mode. |
TargetedPcrMetrics
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon (TSCA) kit (Illumina).
| Field | Description |
|---|---|
| CUSTOM_AMPLICON_SET | The name of the amplicon set used in this metrics collection run |
| GENOME_SIZE | The number of bases in the reference genome used for alignment |
| AMPLICON_TERRITORY | The number of unique bases covered by the intervals of all amplicons in the amplicon set |
| TARGET_TERRITORY | The number of unique bases covered by the intervals of all targets that should be covered |
| TOTAL_READS | The total number of reads in the SAM or BAM file examined |
| PF_READS | The total number of reads passing filter (PF), where the filter(s) can be platform/vendor quality controls |
| PF_BASES | The total number of bases within the PF_READS of the SAM or BAM file to be examined |
| PF_UNIQUE_READS | The number of PF_READS that were not marked as sample or optical duplicates. |
| PCT_PF_READS | The fraction of reads passing filter, PF_READS/TOTAL_READS. |
| PCT_PF_UQ_READS | The fraction of TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS |
| PF_UQ_READS_ALIGNED | The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0 |
| PF_SELECTED_PAIRS | Tracks the number of PF read pairs (used to calculate library size) |
| PF_SELECTED_UNIQUE_PAIRS | Tracks the number of unique, PF, read pairs, observed (used to calculate library size) |
| PCT_PF_UQ_READS_ALIGNED | Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS |
| PF_BASES_ALIGNED | The number of bases from PF_READS that align to the reference genome with mapping score > 0 |
| PF_UQ_BASES_ALIGNED | The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0 |
| ON_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome. |
| NEAR_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region. |
| OFF_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon. |
| ON_TARGET_BASES | The number of PF_BASES_ALIGNED that mapped to a targeted region of the genome. |
| ON_TARGET_FROM_PAIR_BASES | The number of bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome. |
| PCT_AMPLIFIED_BASES | The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED. |
| PCT_OFF_AMPLICON | The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED |
| ON_AMPLICON_VS_SELECTED | The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES) |
| MEAN_AMPLICON_COVERAGE | The mean read coverage of all amplicon regions in the experiment. |
| MEAN_TARGET_COVERAGE | The mean read coverage of all target regions in an experiment. |
| MEDIAN_TARGET_COVERAGE | The median coverage of reads that mapped to target regions of an experiment. |
| MAX_TARGET_COVERAGE | The maximum coverage of reads that mapped to target regions of an experiment. |
| FOLD_ENRICHMENT | The fold by which the amplicon region has been amplified above genomic background. |
| ZERO_CVG_TARGETS_PCT | The fraction of targets that did not reach coverage=1 over any base. |
| PCT_EXC_DUPE | The fraction of aligned bases that were filtered out because they were in reads marked as duplicates. |
| PCT_EXC_MAPQ | The fraction of aligned bases that were filtered out because they were in reads with low mapping quality. |
| PCT_EXC_BASEQ | The fraction of aligned bases that were filtered out because they were of low base quality. |
| PCT_EXC_OVERLAP | The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. |
| PCT_EXC_OFF_TARGET | The fraction of bases that were filtered out because they did not map to a base within a target region. |
| FOLD_80_BASE_PENALTY | The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets. |
| PCT_TARGET_BASES_1X | The fraction of all target bases achieving 1X or greater coverage. |
| PCT_TARGET_BASES_2X | The fraction of all target bases achieving 2X or greater coverage depth. |
| PCT_TARGET_BASES_10X | The fraction of all target bases achieving 10X or greater coverage depth. |
| PCT_TARGET_BASES_20X | The fraction of all target bases achieving 20X or greater coverage depth. |
| PCT_TARGET_BASES_30X | The fraction of all target bases achieving 30X or greater coverage depth. |
| AT_DROPOUT | A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage. After binning the GC content [0..50], we calculate a = fraction of target territory, and b = fraction of aligned reads aligned to these targets for each bin. AT DROPOUT is then abs(sum(a-b when a-b < 0)). For example, if the AT_DROPOUT value is 5% this implies that 5% of total reads that should have mapped to GC<=50% regions, mapped elsewhere. |
| GC_DROPOUT | A measure of how regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage value. For each GC bin [50..100], we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. GC DROPOUT is then abs(sum(a-b when a-b < 0)). For example, if the value is 5%, this implies that 5% of total reads that should have mapped to GC>=50% regions, mapped elsewhere. |
| HET_SNP_SENSITIVITY | The theoretical HET SNP sensitivity. |
| HET_SNP_Q | The Q Score of the theoretical HET SNP sensitivity. |
UmiMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
| Field | Description |
|---|---|
| MEAN_UMI_LENGTH | Number of bases in each UMI |
| OBSERVED_UNIQUE_UMIS | Number of different UMI sequences observed |
| INFERRED_UNIQUE_UMIS | Number of different inferred UMI sequences derived |
| OBSERVED_BASE_ERRORS | Number of errors inferred by comparing the observed and inferred UMIs |
| DUPLICATE_SETS_IGNORING_UMI | Number of duplicate sets found before taking UMIs into account |
| DUPLICATE_SETS_WITH_UMI | Number of duplicate sets found after taking UMIs into account |
| OBSERVED_UMI_ENTROPY | Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. |
| INFERRED_UMI_ENTROPY | Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. |
| UMI_BASE_QUALITIES | Estimation of Phred scaled quality scores for UMIs |