Count: Deletions

• ID: count_deletions
• Description: The number of variant type indels categorized as short deletions (less than 50bp) in VCF, only in autosomal regions, high quality variants.
• Implementation details: In the NPM-sample-QC reference implementation, calculate the number of variant of type indels categorized as deletions in VCF, only in autosomal regions, high quality variants by bcftools view, (bcftools view -H -v indels -f PASS....DEL).
• Type: Integer (eg. 444892)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO vcfqc