@DocumentedFeature public class CrosscheckFingerprints extends CommandLineProgram
| Modifier and Type | Field and Description |
|---|---|
boolean |
ALLOW_DUPLICATE_READS |
CrosscheckMetric.DataType |
CROSSCHECK_BY |
int |
EXIT_CODE_WHEN_MISMATCH |
boolean |
EXPECT_ALL_GROUPS_TO_MATCH |
double |
GENOTYPING_ERROR_RATE |
java.io.File |
HAPLOTYPE_MAP |
java.util.List<java.io.File> |
INPUT |
double |
LOD_THRESHOLD |
double |
LOSS_OF_HET_RATE |
java.io.File |
MATRIX_OUTPUT |
int |
NUM_THREADS |
java.io.File |
OUTPUT |
boolean |
OUTPUT_ERRORS_ONLY |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor and Description |
|---|
CrosscheckFingerprints() |
| Modifier and Type | Method and Description |
|---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static java.util.function.Function<FingerprintIdDetails,java.lang.String> |
getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY) |
static java.util.Map<FingerprintIdDetails,Fingerprint> |
mergeFingerprintsBy(java.util.Map<FingerprintIdDetails,Fingerprint> fingerprints,
java.util.function.Function<FingerprintIdDetails,java.lang.String> by) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="One or more input files (or lists of files) to compare fingerprints for.")
public java.util.List<java.io.File> INPUT
@Argument(shortName="O",
optional=true,
doc="Optional output file to write metrics to. Default is to write to stdout.")
public java.io.File OUTPUT
@Argument(shortName="MO",
optional=true,
doc="Optional output file to write matrix of LOD scores to. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn\'t account for Loss of heterogeneity). It is however sometimes easier to use visually.")
public java.io.File MATRIX_OUTPUT
@Argument(shortName="H",
doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
public java.io.File HAPLOTYPE_MAP
@Argument(shortName="LOD",
doc="If any two groups (with the same sample name) match with a LOD score lower than the threshold the program will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD.\n\nLOD score 0 means equal likelihoodthat the groups match vs. come from different individuals, negative LOD scores mean N logs more likely that the groups are from different individuals, and positive numbers mean N logs more likely that the groups are from the sample individual. ")
public double LOD_THRESHOLD
@Argument(doc="Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be \"rolled-up\" to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE.") public CrosscheckMetric.DataType CROSSCHECK_BY
@Argument(doc="The number of threads to use to process files and generate Fingerprints.") public int NUM_THREADS
@Argument(doc="Allow the use of duplicate reads in performing the comparison. Can be useful when duplicate marking has been overly aggressive and coverage is low.") public boolean ALLOW_DUPLICATE_READS
@Argument(doc="Assumed genotyping error rate that provides a floor on the probability that a genotype comes from the expected sample.") public double GENOTYPING_ERROR_RATE
@Argument(doc="If true then only groups that do not relate to each other as expected will have their LODs reported.") public boolean OUTPUT_ERRORS_ONLY
@Argument(doc="The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via loss of heterozygosity) in the tumor (model assumes independent events, so this needs to be larger than reality).",
optional=true)
public double LOSS_OF_HET_RATE
@Argument(doc="Expect all groups\' fingerprints to match, irrespective of their sample names. By default (with this value set to false), groups (readgroups, libraries, files, or samples) with different sample names are expected to mismatch, and those with the same sample name are expected to match. ") public boolean EXPECT_ALL_GROUPS_TO_MATCH
@Argument(doc="When one or more mismatches between groups is detected, exit with this value instead of 0.") public int EXIT_CODE_WHEN_MISMATCH
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgrampublic static java.util.function.Function<FingerprintIdDetails,java.lang.String> getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY)
public static java.util.Map<FingerprintIdDetails,Fingerprint> mergeFingerprintsBy(java.util.Map<FingerprintIdDetails,Fingerprint> fingerprints, java.util.function.Function<FingerprintIdDetails,java.lang.String> by)