Extracting haplotypes from phased vcf file
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2.8 years ago
siddazra • 0

I have a phased genotype VCF file(i.e haplotype in vcf format). I am interested only in the haplotypes that are there in phased vcf file. Please help or suggest some other way to do it.

haplotype tools • 3.9k views
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what kind of output do you need ?

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I want it in standard haplotype format (.hap)

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2.8 years ago

Hello siddazra,

does bcftools convert with the --hapsample option do what you want?

Other solution is mention in this thread.

fin swimmer

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It worked. I used the command

bcftools convert --hapsample --vcf-ids file.vcf -o output

Thanks.

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Fine :)

I moved my comment to an answer, so you can mark it as accepted.

fin swimmer

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