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
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mostafarafiepour
know how this work is done?
two mutations carried by the same read = phasing
What software is required
GATK HaplotypeCaller does this job.
many thanks for your reply,
But I mean, I want to phasing my VCF file. Because my VCF file is not phasing.
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?
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.
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