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better error messages and --sample-exprs

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@brentp brentp released this 10 Apr 01:46

v0.1.0

  • allow accessing INFO via variant.INFO as well as INFO
  • better error message on missing gnotate file
  • add --sample-expr to slivar expr sub-command to allow applying an expression to each sample:
    --sample-expr "hi_quality:sample.DP > 10 && sample.GQ > 20"
  • expose samples in javascript in $S object, e.g. $S["sampleABC"].DP > 10 && $S["sampleXYZ"].DP > 10
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:v0.1.0

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 (total and controls only) here
  • spliceai scores (maximum value of the 4 scores in spliceai) here