count_deletions

metrics.count_deletions(mqc, biosample_id)

Description: The ratio between number of insertion and deletion 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). Insertions and Deletions are only considered in this metric short, less than 50bp, insertions, deletion as commonly identified by most short reads variant callers. Structural variations which include insertions, deletions larger than 50bp and which are typically identified using dedicated SV callers are not considered.