Detecting compound heterozygous
I'd like to know if my variants are in cis or trans. How can I detect these compound heterozygous individuals? Which tools do you recommend?
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_quantum_girl_ •
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you need a phased VCF.
if your vcf is not phased there are some tools that can be of help: SHAPEIT, Beagle, etc...
I already have phased VCF. I guess my question was how to narrow them down to a list of variants. And then obtain haplotypes like this:
Where 0 is ref and 1 is alt.
I've recently read you can do these with bcftools, just wanted to know if there were other tools out there.