impactful

In short, simply add INFO.impactful && $your_expressions to limit to variants with a higher impact (e.g. excluding synonymous 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 decision is arbitrary, but, given an ordered list of all impacts annotated by existing tools, we can choose a permissive cutoff that still removes a large percentage of variant candidates.

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 "IMPACTFUL_CUTOFF"in the default-order list. If none of CSQ (VEP), BCSQ (bcftools), or ANN (snpEff) are present in the VCF then this attribute is not available.

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".

The order can be customized by copying the default-order.txt file, re-arranging the rows, and setting export SLIVAR_IMPACTFUL_ORDER=/path/to/adjusted-order.txt