The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.

ReadBackedPhasing of trio with 3 bams

sboylesboyle Bay Area, CAMember Posts: 28

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?

Best Answer


  • pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭

    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 Administrator, Dev Posts: 10,739 admin

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

    Geraldine Van der Auwera, PhD

  • pdexheimerpdexheimer Member, Dev Posts: 543 ✭✭✭✭

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

Sign In or Register to comment.