Matt Velinder

I'd throw my support in for DeepVariant integration under `--tools` Is that still a priority? It seemed like it was being worked on back in #105 Thanks!

ExpansionHunter would also be a great addition under `--tools`

If it's not feasible to extend slivar to this compound-het functionality, I was thinking of running slivar twice, once on mother and her parents as a trio. And then take...

Using @brentp 's fix I get the following. Looks like it's just ignoring everything? I get no file written to disk either `bcftools csq -f chm13.draft_v1.1.fasta -g chm13.draft_v1.1.gene_annotation.v4.fix.gff3.gz $VCF -O...

@diekhans To Brent's question, if this is a bcftools problem, what is the recommended way to annotate variant calls on CHM13? Thanks for the guidance!

I got this to work using VEP instead of bcftools csq `vep -gff /path/to/chm13.gff.gz` https://uswest.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gff

Looks like the gene name in the URL is quite straight-forward. Even simply https://decipher.sanger.ac.uk/gene/CDH2 works

You're awesome Tony! This will be super helpful.

octopus also looked very promising https://github.com/luntergroup/octopus https://www.nature.com/articles/s41587-021-00861-3

I continue to think about this feature. The new gene information panel next to the ranked variants table could be an excellent place to put this information. Let's try to...