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] (https://github.com/brentp/slivar/blob/master/src/slivarpkg/default-order.txt) list.

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

INFO.impactful && kid.het && mom.hom_ref && dad.hom_ref && kid.GQ > 10 ...

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.