Laurent ✭✭

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)

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)

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)

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)