Question: Extracting haplotypes from phased vcf file
1
gravatar for siddazra
3 months ago by
siddazra0
siddazra0 wrote:

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 • 396 views
ADD COMMENTlink written 3 months ago by siddazra0

what kind of output do you need ?

ADD REPLYlink written 3 months ago by Pierre Lindenbaum112k

I want it in standard haplotype format (.hap)

ADD REPLYlink written 3 months ago by siddazra0
2
gravatar for finswimmer
3 months ago by
finswimmer5.4k
Germany
finswimmer5.4k wrote:

Hello siddazra,

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

Other solution is mention in this thread.

fin swimmer

ADD COMMENTlink modified 3 months ago • written 3 months ago by finswimmer5.4k

It worked. I used the command

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

Thanks.

ADD REPLYlink modified 3 months ago by finswimmer5.4k • written 3 months ago by siddazra0

Fine :)

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

fin swimmer

ADD REPLYlink written 3 months ago by finswimmer5.4k
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