Ratio: Insertions/Deletions

• ID: ratio_insertion_deletion
• Description: The ratio between number of short insertion and deletion (less than 50bp) in VCF, only in autosomal regions, high quality variants.
• Implementation details: In the NPM-sample-QC reference implementation, calculate the ratio of insertions and deletion in VCF, only in autosomal regions, high quality variants by bcftools view, (bcftools view -H -v indels -f PASS....INS / bcftools view -H -v indels -f PASS....DEL).
• Type: Float 2 decimal precision (eg. 1.13)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO vcfqc