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v0.2.2
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@brentp brentp released this 12 May 17:42
v0.2.2
186b862

This release is mostly minor or obscure bug-fixes with several usability improvements and fixes in compound-hets..

v0.2.2

  • fix bug with '.' in ALT field (caused message about incorrect number of alts in some cases. thanks Batsal for reporting)
  • slivar compound-hets: fix bug with parents specified in ped file but absent from VCF (#79)
  • slivar compound-hets: add "intergenic_region" to list of impacts that are skipped by default
  • add SLIVAR_NO_REPORT_ALL to prevent reporting variants for familys with no affected samples
  • fix bug when creating huge zip files with make-gnotate (#86)
  • NOTE: change default min depth in slivar-functions.js to 6. (was 0)
  • don't hard-code tmp directory to /tmp (use $TMPDIR)
  • [compound-hets] dont fail if no usable variants were found, just issue warning.
    this can happen for small chroms or regions when slivar was parallelized.

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:v0.2.2
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:

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