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MergeBatchSites

WDL source code

Merges variants across batches. Variants are merged only if the following attributes match exactly:

  • Contig
  • Start position
  • End position (END field)
  • SV type (SVTYPE field)
  • SV length (SVLEN field, if available)
  • Strandedness (STRANDS field, if available)
  • Second contig (CHR2 field, if available)
  • Second end (END2 field, if available)

This is a "cohort-level" workflow, meaning that is aggregates data across all batches. This is in contrast to all previous modules, which are sample- or batch-level. Note that this workflow should still be run on cohorts consisting of a single batch.

info

Terra users must configure a "sample_set_set" in their data table before running this module. See the Execution section on MergeBatchSites for futher instructions.

The following diagram illustrates the recommended invocation order:

Inputs​

cohort​

An identifier for the cohort. The guidelines outlined in the sample ID requirements section apply here.

depth_vcfs​

Array of filtered depth VCFs across batches generated in FilterBatch.

pesr_vcfs​

Array of filtered depth VCFs across batches generated in FilterBatch.

Outputs​

cohort_pesr_vcf​

Merged PE/SR caller VCF.

cohort_depth_vcf​

Merged depth caller VCF.