Question: Phasing Confidence Values using Shapeit2
gravatar for Mike Vermeulen
2.1 years ago by
Mike Vermeulen0 wrote:

Hello everyone,

I have 12 singleton WGS samples that I am trying to phase using Shapeit2 using the reference panel method from 1000 genomes. I can successfully run the program and finish with a vcf containing estimated haplotypes for each variant. However, I'm looking for a confidence value on each so I can filter on a strict threshold.

Is there an argument or a simple method that can be used to extract haplotype phasing probability estimates and add them to the vcf file?

Any tips on WGS phasing using shapeit would be great.


ADD COMMENTlink written 2.1 years ago by Mike Vermeulen0

Hello, I was wondering if you solved this or not as I have the same question. Thank you for any suggestions or insight that you might have. Best regards, Janet

ADD REPLYlink written 11 months ago by janetw0
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