Ratio: Heterozygous/Homozygous (indels)

• ID: ratio_heterozygous_homzygous_indel
• Description: The ratio of heterozygous and homozygous variant of type indels in VCF, only in autosomal regions, high quality variants.
• Implementation details: In the NPM-sample-QC reference implementation, calculate the ratio of heterozygous and homozygous variant of type indels in VCF, only in autosomal regions, high quality variants by bcftools view, (bcftools view -H -v indels -f PASS -g het / bcftools view -H -v indels -f PASS -g hom).
• Type: Float 2 decimal precision (eg. 2.02)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO vcfqc