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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR with SNP calls? #173

Open markdunning opened 1 year ago

markdunning commented 1 year ago

Hello,

I'm looking for a way to merge my SNP calls from different callers, and identify and SNPs identified from at least 2 of 3 callers to give me more confidence in my results.

I haven't yet found a convenient tool for doing this, and wonder if SURVIVOR would work? If so, what would be the appropriate settings since most of my variants will be 1 in length. I've been experimenting with different options, but I only seem to get variants with length > 1 in my merged output.

Cheers, Mark

Akazhiel commented 1 year ago

Not the developer or related in any way with this project but thought I could pitch in since we do this on a daily basis on our pipeline. For the use case you describe, we use the CombineVariants tool that's present on GATK 3.8. Since it was discontinued after GATK4 you'd need to download this version's jar and run it from there.

Cheers, Jonatan

fritzsedlazeck commented 1 year ago

Thanks. Yeah survivor is really only for structural variants.. so no on snv. There are multiple tools for snv merging/comparison. The easiest might be bcftools.