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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Quickstart should contain info on how to create a pedigree file and what tool is recommended for combining trio VCF into single file #156

Closed nurmians closed 11 months ago

nurmians commented 11 months ago

I wanted to give slivar a try with my trio variant calls, but there is no information on how to create a pedigree file and how to combine multiple VCFs. I know there are many tools for that, but to minimize risk of incompatibility you should mention a tool that is tested to be compatible. For example, can I use annovar annotated VCF files?

brentp commented 11 months ago

Hi, I pushed a fix for the documentation of pedigree format. slivar does not support effects added by annovar. You'll have to use VEP, snpEff, or bcftools. You'll also need a single, jointly-called VCF, not ones that have been called separately and then merged.