This app runs a python script to calculate the mean het, mean hom and het:hom ratio of non reference variants in a given vcf. Alternate heterozygous variants (i.e. those with a genotype of 1/2) are not included in the mean het or het:hom ratios.
This app should be executed stand-alone or as part of a DNAnexus workflow for a single sample.
The app requires a VCF file (.vcf) containing variants to be evaluated and a bed file defining the regions within which variants in the vcf should be evaluated.
The app outputs one tab delimited file [vcf_prefix].vcf.QC, where vcf_prefix is the vcf filename without extension:
- sample id
- mean het ratio (mean AAF of het variants)
- mean hom ratio (mean AAF of hom variants)
- het:hom ratio (ratio of het to hom variants on autosomes)
- X het:hom ratio (ratio of het to hom variants on chrX)