This adds small improvements except for large bug-fix for compound-hets for families with multiple affected kids. Previously, a shared compound-het would only be reported for one of the kids. This now fixed. See below for full changelog.

v0.1.12

• slivar expr: handle ploidy > 2 (updated hts-nim) (#55 thanks to @markw3lsh for reporting and providing a test-case)
• slivar: optionally support strings in format (sample) fields. default is to ignore these for performance reasons, but users can set the environment variable SLIVAR_FORMAT_STRINGS to anything to force slivar to populate the javascript objects with any strings in the VCF. e.g. SLIVAR_FORMAT_STRINGS=1 slivar expr ... and use unset SLIVAR_FORMAT_STRINGS to remove. (#37)
• slivar compound-hets: fix bug with 2 affect sibs sharing same compound-het previously only 1 sib would be reported

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. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.1.12

The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
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

• gnomad genomes (71,702 samples) for hg38 with AF popmax, numhomalts (updated in release v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37