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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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gnotate: converting BED to VCF #144

Closed wwgordon closed 10 months ago

wwgordon commented 2 years ago

Hi Brent,

I'm working on setting up a slivar pipeline with @jxchong; we have a number of annotation files that are bed formatted rather than vcf/bcf. Do you have a recommended tool for conversion? plink perhaps?

Thanks, William

brentp commented 2 years ago

Hi William (and Jessica), is the data of sequence-resolved variants? are there millions of variants? If so, then it makes sense to use gnotate. In that case, you'd have to write a script in python to do that. I have an example doing this for CADD (with another tool you might consider) here

If you have few sites or not variants with REF and ALT, then just use vcfanno.

wwgordon commented 10 months ago

Closing this as we have been successful in incorporating bed files, thanks!