impactful

In many cases, an analyst will want to limit to variants that are of a higher impact. This is facilitated in part by the tsv sub-tool which reports the highest impact in each variant by parsing the CSQ and using an ordered list of impacts seen in VEP, bcftools and snpEff.

In order to expose a simple way for the user to do minimal filtering on the highest impact in the CSQ, we have added in version 1.6 INFO.impactful this value is true if any impact in the variant falls above the sentinel value of "IMPACT_CUTOFF"in the default-order list.

This means that, given a VCF with CSQ or BCSQ fields, a reasonable adjustment de novo filter for rare disease could be:

INFO.impactful && kid.het && mom.hom_ref && dad.hom_ref && kid.GQ ...

This will, of course, exclude any synonymous variants, but this can be helpful as a first-pass, especially in whole-genomes where the number of candidates is much larger.