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Combining PhaseByTransmission and ReadBackedPhasing

Hello GATK Team,

there are currently two walkers for phasing in the GATK PhaseByTransmission and ReadBackedPhasing.
Because of their different information source (PhaseByTransmission has the called VCF file, ReadBackedPhasing the BAM files) these can produce different or complementary genotypes.
There used to be a walker for this job "MergeAndMatchHaplotypes" but it seems to be discontinued.

What is the current recommendation for Trios?
Only use PhaseByTransmission?

Best Answer

  • LaurentLaurent Member, Broadie
    Accepted Answer

    Hi Bernt,

    You can use PhaseByTransmission first and then use ReadBackedPhasing with the --respectPhaseInInput option. This will respect the previous phase from PhaseByTransmission but phase sites with ReadBackedPhasing where possible.

    Cheers,
    Laurent

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