search

KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
113 stars 27 forks source link

GQ and gnomad3_counts annotator module #126

Closed PabloRomanjo closed 7 months ago

PabloRomanjo commented 1 year ago

Dear Cravat team,

First of all, thank you very much for this fantastic tool, I am using it a lot.

I have two questions/doubts/suggestions:

  1. Is it possible to annotate the GQ value from vcfinfo? I found that we can annotate AC (extra_vcf_infoAC), DP (extra_vcf_infoDP), MQ, QD, MLEAF, ExcessHet ... (and others) but not GQ.

  2. The second is related to the gnomad3_counts annotator module. I have been investigating on it, and I think that it is only possible to annotate the count of homozygotes for a certain position (for example, using gnomad3_counts__nfe). I do not know exactly the utility of this, but I think it could be easily improved if, instead of (or in a complementary way to) the count of homozygous, this annotator would return the total alt_allele count (count of alt homozygous 2 + count of heterozygous) and ref_allele count ref_allele count (ref homozygous 2 + count of heterozygous) for the variant position. These numbers would allow to perform further analysis.

Again, thank you very much for your efforts.

Pablo Román-Naranjo Varela Otology & Neurotology Group CTS495 Genomic Medicine Area Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO) Granada | Spain

mlarsen2 commented 1 year ago

It's great to hear that you are enjoying OpenCRAVAT!

In response to your question about the GQ value, in the Extra VCF INFO Annotations section there should be 2 fields for "GQ_mean" and "GQ_STDDEV". If you do not see them there, feel free to send us your input file and we can see what's going on.

The gnomad3_counts annotator does only count the homozygotes, and your suggestion of the total alt and total ref counts would be a great addition. We will update you when the new counts have been implemented into OpenCRAVAT!