impactful

In short, simply add INFO.impactful && $your_expressions to limit to variants with a higher impact (e.g. excluding synonmous and intronic). No additional files or flags are required to use this feature.

Often, 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 (VEP), BCSQ (bcftools), or ANN (snpEff) 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.

If CSQ, BCSQ, and ANN are all present, slivar will check if any of them contain an impact high enough to be called "impactful".