Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Laurent ✭✭
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Re: Step order for PhaseBytransmission and ReadBackedPhasing
Hi Erika, The genotype change that you see between steps (1) and (2) is due to the relatively limited evidence for a de novo mutation when taking the prior probability for a de novo mutation to happe… (View Post) -
Re: Step order for PhaseBytransmission and ReadBackedPhasing
Hi Erika, At the moment there is no tool within the GATK to infer the parent of origin for de novo mutations. Basically what needs to be done is to go through the entries and "follow" each … (View Post) -
Re: Error with the HaplotypeCaller when genotyping given alleles
Regarding the BUG: GenomeLoc issue, I found out the problem: I had the "END" annotation with the wrong coordinates in my VCF for some positions. I am not sure where it happened in the pipel… (View Post) -
Re: Combining PhaseByTransmission and ReadBackedPhasing
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 wit… (View Post)
