Extracting haplotypes from phased vcf file

Question

[siddazra]

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.

[Pierre Lindenbaum]

what kind of output do you need ?

[siddazra]

I want it in standard haplotype format (.hap)

Answer 1

[finswimmer]

Hello siddazra,

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

Other solution is mention in this thread.

fin swimmer

[siddazra]

It worked. I used the command

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

Thanks.

[finswimmer]

Fine :)

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

fin swimmer