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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Homozygous reference variants #209

Closed kkmarkel closed 5 months ago

kkmarkel commented 5 months ago

Hello!

I have a question - does Open-CRAVAT annotate homozygous reference (0/0) variants? Is there any way to include them into annotation results?

jasminebro commented 5 months ago

Hi @kkmarkel. OpenCravat does not annotate 0/0 variants. If you are using a local installation of OpenCravat, you can look at the input_filename_vcf.err file in your job directory to see which lines were skipped.

A work around could be to edit the vcf and add a fake sample that 1/1 for every variant.