compound-hets on non trios and error messages

brentp released this 24 Jun 16:14

d25421d

v0.1.4

better error messages on bad VCF
[tsv] add --csq-column to slivar tsv to allow extracting extra CSQ fields
general usability improvements
[compound-het]: support singleton (kid only) or duo's (kid and 1 parent) to compound het. this will give many false positives because
the variants can't be phased, but the number can still be quite small given sufficient filtering on population allele frequency.
requires --allow-non-trios argument

binaries and docker

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.

users can also use slivar via docker at brentp/slivar:v0.1.4

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
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

Assets 3