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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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make-genotate genomes files #99

Closed skanwal closed 3 years ago

skanwal commented 3 years ago

Hello @brentp

Firstly, thanks for this resource.

To provide context, I have a tumour-only VCF for a cancer sample that I'd like to filter out for likely false variants. I am exploring slivar to see if we can leverage population frequency to help with noise reduction in sample VCF.

Reading through wiki, I wanted to ask the best way to get gnomad.genomes.r2.1.sites.chr*.vcf.bgz. Looking through the gnomad website, noticed there are quite huge individual files for all chromosomes (v3.1 as I am working with genome build 38). Do we need to download these for creating custom gnotate files?

UPDATE: Noted slivar comes with gnomad files for hg38 - giving these a try with my sample VCF for filtering variants.

Help will be appreciated. Thanks.

brentp commented 3 years ago

Hi, let me know if you need further help, you should be able to use the provided zip files for hg38, but yes, if you want to make your own gnotate zip files you'll need to download all of the gnomad vcfs.

skanwal commented 3 years ago

Thank you. Closing this for now as I was able to to use the provided gnomad files.