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GenotypeBatch

Genotypes a batch of samples across unfiltered variants combined across all batches.

Prerequisites​

  • Filter batch
  • Merge Batch Sites

Inputs​

  • Batch PESR and depth VCFs (FilterBatch)
  • Cohort PESR and depth VCFs (MergeBatchSites)
  • Batch read count, PE, and SR files (GatherBatchEvidence)

Outputs​

  • Filtered SV (non-depth-only a.k.a. "PESR") VCF with outlier samples excluded
  • Filtered depth-only call VCF with outlier samples excluded
  • PED file with outlier samples excluded
  • List of SR pass variants
  • List of SR fail variants
  • (Optional) Depth re-genotyping intervals list