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Input Data

GATK-SV requires the following input data:

  • Illumina short-read whole-genome CRAMs or BAMs, aligned to hg38 with bwa-mem. BAMs must also be indexed.

  • Family structure definitions file in PED format.

PED file format​

The PED file format is described here. Note that GATK-SV imposes additional requirements:

  • The file must be tab-delimited.
  • The sex column must only contain 0, 1, or 2: 1=Male, 2=Female, 0=Other/Unknown. Sex chromosome aneuploidies (detected in EvidenceQC) should be entered as sex = 0.
  • All family, individual, and parental IDs must conform to the sample ID requirements.
  • Missing parental IDs should be entered as 0.
  • Header lines are allowed if they begin with a # character. To validate the PED file, you may use src/sv-pipeline/scripts/validate_ped.py -p pedigree.ped -s samples.list.

Sample Exclusion​

We recommend filtering out samples with a high percentage of improperly paired reads (>10% or an outlier for your data) as technical outliers prior to running GatherSampleEvidence. A high percentage of improperly paired reads may indicate issues with library prep, degradation, or contamination. Artifactual improperly paired reads could cause incorrect SV calls, and these samples have been observed to have longer runtimes and higher compute costs for GatherSampleEvidence.

Sample ID requirements​

Sample IDs must​

  • Be unique within the cohort
  • Contain only alphanumeric characters and underscores (no dashes, whitespace, or special characters)

Sample IDs should not​

  • Contain only numeric characters
  • Be a substring of another sample ID in the same cohort
  • Contain any of the following substrings: chr, name, DEL, DUP, CPX, CHROM

The same requirements apply to family IDs in the PED file, as well as batch IDs and the cohort ID provided as workflow inputs.

Sample IDs are provided to GatherSampleEvidence directly and need not match sample names from the BAM/CRAM headers. GetSampleID.wdl can be used to fetch BAM sample IDs and also generates a set of alternate IDs that are considered safe for this pipeline; alternatively, this script transforms a list of sample IDs to fit these requirements. Currently, sample IDs can be replaced again in GatherBatchEvidence.

The following inputs will need to be updated with the transformed sample IDs: