ReadBackedPhasing --respectPhaseInput

Answers

• Sheila Broad InstituteMember, Broadie, Moderator admin

  March 2015

  @dmyersturnbull
  Hi Douglas,

  You no longer need to use ReadBackedPhasing. HaplotypeCaller does physical phasing for you. We only use ReadBackedPhasing for merging MNPs. The updated slides from our latest workshop are here: https://www.broadinstitute.org/gatk/blog?id=5338

  It is true the --respectPhaseInput argument is gone. We will check with the developers on what the current behavior is for dealing with phased input.

  -Sheila

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• dmyersturnbull Stanford UniversityMember ✭

  March 2015

  Hi Sheila,

  I'd forgotten that about HaplotypeCaller.

  Will PhaseByTransmission respect previous phasing or use it as evidence? I noticed that HaplotypeCaller uses the annotations PID and PGT rather than GT (I never see a | in the GT from HC). Does PBT use those?

  I'm trying to use ShapeIt2 for phasing, but it can't phase variants that aren't in the reference panel (1000G phase 3), so I'm hoping to fill those in afterward using PBT and either RBP or HC's PGT annotations. Filling in the unphased GTs using PGT annotations seems like it could result in inconsistent haplotypes, so I'm wondering whether PBT and RBP can "build off of" ShapeIt2's partial phasing. That's why I'm interested in this.

  Thanks,
  Douglas

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  March 2015

  @dmyersturnbull PhaseByTransmission doesn't know about HC's phasing tags, so it will neither take them into account nor change them in any way. The fact that they store the phasing information in different forms is done on purpose to avoid collisions.

  I looked briefly at the PBT and RBP code but it wasn't obvious to me how the tools treats incoming phasing info. The phasing tools are developed by external collaborators, @mfromer and @Laurent -- hopefully they can have a look and answer your questions. If not I'll try to hunt down the answer from the rest of the team next week.

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• Laurent Member, Broadie ✭✭

  April 2015 Accepted Answer

  Hi @dmyersturnbull,

  PhaseByTransmission operates on a site-by-site basis, so it will be totally blind to previous phasing annotation. You can of course phase sites with PBT and then merge them with the previous phasing, but this will require a little file manipulation. Note that if you're willing to get your hands dirty, it would be very easy to add a line in the PBT code so that it doesn't process previously-phased sites. Although it would be best for Menachem to respond, I believe that when using RBP with the --respectPhaseInput option will indeed only phase sites that weren't previously phased and do so while respecting previous annotations.

  Cheers,
  Laurent

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• dmyersturnbull Stanford UniversityMember ✭

  April 2015

  Thanks, @Sheila, @Geraldine_VdAuwera, and @Laurent. That clears it up completely!

  Best,
  Douglas

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