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mebbert / VariantToolChest

VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful tools: (1) SetOperator for performing powerful set operations; and (2) VarStats for various statistics on VCF files.
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"Enhanced Compare" question #6

Open djakubosky opened 7 years ago

djakubosky commented 7 years ago

Not so much an issue, but rather a question. Came across your BMC Bioinf paper, I am attempting to compare genotype concordance between samples (monozygotic twins) in a vcf (similar to your description of an "enhanced compare"), is there an approach to doing this using VTC? Is there a way you suggest? I am finding other tools such as bcftools unable to accomplish this in a large vcf. Thanks for your help, nice tool!

mebbert commented 7 years ago

@djakubosky,

Sorry for the slow response. Doing a strict concordance was a planned feature for VTC that we never got around to implementing. It wouldn't be very hard to implement, but we don't currently funding to maintain VTC.

There is also one major design flaw I made when I first wrote VTC: I read everything into memory. This works great on small data sets, but quickly gets unwieldy on whole-genome stuff. What was I thinking? It's a mystery. :-P This is also easy to fix, but I don't currently have the bandwidth to update it.

Sorry I don't have better news for you. If, however, you have someone that could spend a bit of time implementing it, I'd be happy to guide him/her.