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Extracting haplotypes from phased vcf file

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
• 9,172 views • link
updated by Ram Ram • written by siddazra • siddazra

I want it in standard haplotype format (.hap)

• 1 views • link
written by siddazra • siddazra

1 answer

Hello siddazra,

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

Other solution is mention in this thread.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

It worked. I used the command 

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

Thanks.

• 1 views • link
updated by finswimmer finswimmer • written by siddazra • siddazra

Fine :)

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

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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