count_insertions

metrics.count_insertions(mqc, biosample_id)

Description: The number of variant type indels only insertions in VCF, only in autosomal regions, high quality variants.

Implementation details: In the NPM-sample-QC reference implementation, calculate the number of variant type indels only insertions in VCF, only in autosomal regions, high quality variants by bcftools view, (bcftools view -H -v indels -f PASS….INS). Insertions are only considered in this metric short, less than 50bp, insertions as commonly identified by most short reads variant callers. Structural variations which include insertions larger than 50bp and which are typically identified using dedicated SV callers are not considered.