Question: How to phase a vcf file
0
gravatar for mostafarafiepour
23 months ago by
mostafarafiepour60 wrote:

Hi

I want to Phasing VCF file. But I do not know how this work is done? What software is required? I only know that the Beagle can be used. But I do not know what command lines are needed.

mostafa

snp • 1.6k views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum127k • written 23 months ago by mostafarafiepour60
1
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

know how this work is done?

two mutations carried by the same read = phasing

What software is required

GATK HaplotypeCaller does this job.

ADD COMMENTlink written 23 months ago by Pierre Lindenbaum127k

many thanks for your reply,

But I mean, I want to phasing my VCF file. Because my VCF file is not phasing.

ADD REPLYlink written 23 months ago by mostafarafiepour60

I've created a VCF file with using GATK. I have also done the filtering steps. And in fact it is a final VCF file. So, The next step is to phasing you right?

ADD REPLYlink written 23 months ago by mostafarafiepour60

I've created a VCF file with using GATK.

as far as I remember HaplotypeCaller puts a FORMAT field named PGT for phased genotypes. Of course, if your reads are too short or your variants are not close to each other, there will be no phasing.

ADD REPLYlink written 23 months ago by Pierre Lindenbaum127k
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