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make gnotate

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Brent Pedersen edited this page Apr 5, 2021 · 6 revisions

make-gnotate is used to create new gnotation (zip) files to be used by slivar.

Usage is mostly straight-forward. For example, to create the gnomad*.zip files, we use something like:

slivar make-gnotate \
    --field AF_POPMAX:gnomad_popmax_af \
    --field Hom:gnomad_nhomalt \
    --prefix gnomad.hg38 \
     gnomad.exomes.r2.0.1.sites.GRCh38.noVEP.norm.bcf \
     gnomad.genomes.r2.0.1.sites.GRCh38.noVEP.norm.bcf

which takes the AF_POPMAX and Hom fields from the genomes and exomes VCFs and names them gnomad_popmax_af and gnomad_nhomalt respectively. These names (following the ':') should be chosen carefully as they will be the field added to the INFO whenever this is used as an annotator.

The resulting file will be gnomad.hg38.zip

Limitations

  1. Fields added to the zip must be float or integer fields
  2. In some cases, we may want to modify a field before adding it to the VCF. This must be done before using make-gnotate.
  3. You must concatenate per-chromosome files into a single file (bcftools concat can do this quickly) before sending to make-gnotate.

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