Skip to main content

MakeCohortVcf

Combines variants across multiple batches, resolves complex variants, re-genotypes, and performs final VCF clean-up.

Prerequisites​

  • GenotypeBatch
  • (Optional) RegenotypeCNVs

Inputs​

  • RD, PE and SR file URIs (GatherBatchEvidence)
  • Batch filtered PED file URIs (FilterBatch)
  • Genotyped PESR VCF URIs (GenotypeBatch)
  • Genotyped depth VCF URIs (GenotypeBatch or RegenotypeCNVs)
  • SR pass variant file URIs (GenotypeBatch)
  • SR fail variant file URIs (GenotypeBatch)
  • Genotyping cutoff file URIs (GenotypeBatch)
  • Batch IDs
  • Sample ID list URIs

Outputs​

  • Finalized "cleaned" VCF and QC plots