ReadBackedPhasing of trio with 3 bams

sboylesboyle Posts: 22Member

I have applied PhaseByTransmission on a trio with a ped file and now want to run ReadBackedPhasing. However, each of the trio variant calls were called from a different BAM file (as each was from a different individual). In the ReadBackedPhasing documentation it only mentions using the program with a single bam. Does this mean that I need to merge the bams for each of the three individuals into a single bam? If so, do you have any suggested programs that work well with GATK?

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  • pdexheimerpdexheimer Posts: 419Member, GSA Collaborator ✭✭✭✭

    No, the documentation is just presenting the simplest case. Most if not all GATK tools that accept bam files will take any number - just specify -I multiple times or give it a text file listing all the BAMs

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,190Administrator, GATK Developer admin

    And once more, @pdexheimer swoops in with a helpful answer before I notice :)

    Geraldine Van der Auwera, PhD

  • pdexheimerpdexheimer Posts: 419Member, GSA Collaborator ✭✭✭✭

    Just beat you to the post button, that's all. @sboyle, don't forget to include the -respectPhaseInInput argument

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