Count: SNVs

• ID: count_snvs
• Description: The number of variant of type SNVs 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 SNVs in VCF, only in autosomal regions, high quality variants by bcftools view, (bcftools view -H -v snps -f PASS).
• Type: Integer (eg. 3906868)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO vcfqc