slivar
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brentp
genetic variant expressions, annotation, and filtering for great good.
Hi @brentp, I ran the comphet function after calling the denovo and comp-side, and it gave me fatal error that I don't know how to fix. I have ran the...
Hi @brentp I am having the same issue reported on [issue#94](https://github.com/brentp/slivar/issues/94). I downloaded gnomad v3.1.1, and concat all the chr VCF into one file, around 2.3T. I used following command...
Hi. I've been using your software to perform a pedigree study of whole genome sequencing data.I drew histograms of AB and GQ using Slivar DDC, and next I had a...
Hi @brentp, Is this possible for slivar to write in output what kind of compound het is this? I mean _in cis_ or _in trans_. For now I need to...
would be nice to have an OSX binary for the next release. Can probably figure out how to have travis-ci build and upload it.
Hi @brentp, Is it possible for slivar to allow VEP's canonical flag in the CSQ field when exporting to tsv? E.g. gene_impact_transcript_Gene_CANONICAL_EXON_HGVSc_HGVSp_Protein_position_Consequence_PolyPhen_SIFT Thanks, Madeline
currently slivar tsv only works on trios (and duos, I think). It would be nice to make it work with groups. See #88
Hi Brent I notice that in .js file recommended for the rare diseases best practices pipeline, you have segregating-dominant, segregating-recessive and segregating-denovo functions, yet the pipeline just calls segregating-recessive and...
I made some gnotate files for the CADD. This is using slivar 0.2.1. I first transformed the cadd tsv files to vcf (using your old cadd2vcf.py script from vcfanno) then...
Hi Brent, I am running an expression like below. ./slivar expr --vcf sample_merged_denovo_SIZEGT300_SETGT.vcf --ped family.ped --out-vcf temp.vcf --group-expr "denovo:kida.alts != 0 && kidb.alts != 0 && mom.alts == 0 &&...
