bugfix 0.2.8 regression for annotation
v0.3.0
- bugfix for 0.2.8 regression where SNPs present in gnotate file would be instead annotated as missing #149.
This happened when annotating a chromosome after a chromosome present in the query set that was not in the gnotate file
Thanks very much to Steve @seboyden for reporting and providing a test-case.
Installation
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:v0.3.0
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
