In previous versions, there was a slivar gnotate sub-command. This has now been enveloped into slivar expr so a user can specifiy, e.g. slivar expr -g gnomad.hg37.zip -i "INFO.gnomad_popmax_af < 0.001" $vcf (and of course slivar expr still supports --sample-expr, --trio, and --group exressions).

v0.1.3

• add new sample attributes hom_ref, het, hom_alt, unknown which are synonyms of alts == 0, alts == 1, alts == 2, alts == -1 respectively.
• remove slivar gnotate sub-command. the same functionality can be had from slivar expr with -g and --info.

binaries and annotation files

There are 2 binaries for this release. Both are 64bit linux binaries.

• slivar_static is a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.
• slivar_shared depends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.

users can also use slivar via docker at brentp/slivar:v0.1.3

the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

• gnomad for hg37 with AF popmax, numhomalts (total and controls only) here
• gnomad for hg38 with AF popmax, numhomalts (updated in release v0.1.2) here
• spliceai scores (maximum value of the 4 scores in spliceai) here