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ReGenotypeCNVs

Re-genotypes probable mosaic variants across multiple batches.

Prerequisites​

  • Genotype batch

Inputs​

  • Per-sample median coverage estimates (GatherBatchEvidence)
  • Pre-genotyping depth VCFs (FilterBatch)
  • Batch PED files (FilterBatch)
  • Cohort depth VCF (MergeBatchSites)
  • Genotyped depth VCFs (GenotypeBatch)
  • Genotyped depth RD cutoffs file (GenotypeBatch)

Outputs​

  • Re-genotyped depth VCFs.