until this release slivar was heavily focused on trio expressions. but this left quads and more ragged families as possible but more difficult. this release allows things like:

--family-expr 'aff_only:fam.every(function(s) { s.het == s.affected && s.hom_ref == !s.affected && s.GQ > 15 })'

to extract variants where all affecteds in a family are heterozygotes and all unaffecteds are homozygous reference (and all samples have genotype quality > 15).

This release also introduces INFO.impactul, which is extracted from the consequence field added by VEP, bcftools, or snpEff (or all of them if they are all present). This can be used to exclude, for example synonymous or non-coding or other variants as a way to quickly get candidate variants that are more likely functional. See the wiki for more details.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.6

Full release notes:

v0.1.6

• add INFO.impactful (boolean) if CSQ/BCSQ/ANN is present. this value will be true of any of those annotation are high enough
• the impactful flag is automaticaly added to the output VCF for any variant passing through slivar and meeting the criteria (https://github.com/brentp/slivar/wiki/impactful)
• better checks for length of AD field
• fix for empty groups (#38)
• add --family-expr for family expressions like:
  fam.every(function(s) { s.het == s.affected && s.hom_ref == !s.affected && s.GQ > 5 })
• slivar tsv now outputs a sortable column for highest-impact. it makes use of a default
  list of impact orderings from: https://uswest.ensembl.org/info/genome/variation/prediction/predicted_data.html and
  supplemented with any type seen in bcftools or snpEff.
• bug fix with gnotate (-g) when annotating a file with a empty chromsome followed by a non-empty (e.g. if chr16_random is mixed in with canonical chromosomes)