This release is the first where pslivar (parallel slivar) is well tested. It handles running slivar expr in parallel (by genomic region) see wiki page for more detail.

This also adds INFO.genic for VCFs that have been annotated with VEP, snpEff, or bcftools. This complements INFO.impactful, but mainly adds synonymous variants to consideration. See the wiki for more detail.

Full changes below:
v0.1.11

• gnotate: ~10-20% speed improvement by inlining cmp in binarysearch
• slivar expr: fix counts in summary table when some families in the cohort have no affected samples
• slivar tsv: improve readability when 1 or both parents are missing
• slivar tsv: fix comma separation with 1 or both parents missing (thanks @brwnj for reporting)
• slivar ddc: when looking at all chromosomes, skip X, Y
• slivar expr: add --exclude option which takes a bed file of exclude regions
• slivar compound-hets: default will now output compound-het pairs that include synonymous variants
• pslivar: fix tsv output from pslivar (which allows running slivar in parallel). more info here
• add INFO.genic boolean to complement INFO.impactful. By default this includes all impacts included by impactful along with
  synonymous and other exonic, but non-protein-altering variants (but does not include intronic. (more info here

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:v0.1.11

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