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Published 20 hours ago • verified publisher icon sgkit-dev

VCF file for alleles = 2

Open shy218 opened this issue 4 years ago • 1 comments

I currently have the testing VCF file, but the number of alleles is 4. Do you have any dataset with alleles as 2? Or do we have functions, (like filter in Hail) to convert the alleles to 2 by deleting all the variants with alleles 4?

shy218 avatar Apr 23 '21 10:04 shy218

Hey @shy218, you could try hail.methods.split_multi_hts. That would let you create a new VCF with only bi-allelic variants without losing any of the original variants. We don't have anything for that in sgkit yet.

eric-czech avatar Apr 23 '21 11:04 eric-czech