How to phase a vcf file

Question

[mostafarafiepour]

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

Answer 1

[Pierre Lindenbaum]

know how this work is done?

two mutations carried by the same read = phasing

What software is required

GATK HaplotypeCaller does this job.

[mostafarafiepour]

many thanks for your reply,

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

[mostafarafiepour]

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?

[Pierre Lindenbaum]

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.