is it possible to Improve the Phasing of Family Trios using both GATK PhaseByTransmission and ReadBackedPhasing?
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5.5 years ago
shajib.sust ▴ 40

Hi,

I observed that PhaseByTransmission (PBT) can not define the phasing of every genotypes (due to ambiguity) for a family trio. Whereas, ReadBackedPhasing (RBP) can show physical phasing of each individual person. So, my question was can we use both the information of PBT and RBP for a set of loci to identify the phasing of the genotypes (especially for the 'hets') for which PBT could not decide the phasing (within that set of loci)? Is there any existing algorithm or tools to do this for a family trio? 

Another query from my side is: How does ReadBackedPhasing define the chromatid number for a set of haplotypes of a person? As I am a new researcher in this field, I will be very grateful to get any clarification for these queries...

With Kind Regards,
-Ruhul

Phasing ReadBackedPhasing latest GATK Tool • 1.8k views
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