steveb

We want to try using MuTect2 on FFPE genomes. Should the panel of normals be made of up FFPE normals?

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steveb
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  • Okay but doesn't each sample have have a ploidy_priors_table (...counts.tsv) generated by CollectReadCounts earlier? So now when I try to run DetermineGermlineContigPloidy for the cohort it requires one of these tables. Do I combine them some how…
  • I used miniconda to install the gatk environment. I do not see that gcnvkernel is installed. But I CANNOT also install it from anywhere. I am also trying to run germline CNV tools. Any advice?
  • Okay thanks, I read over the blog. In regards to the suggestion "... the new FilterAlignmentArtifacts tool is useful when even more stringent filtering is needed..." we would like GATK's opinion on if this tool can be be used in conjun…
  • I should clarify that the samples would be tumour only FFPE. I have used the new recommended workflow: 1.) The new tool is CollectF1R2Counts and LearnReadOrientationModel 2.) The output of LearnReadOrientationModel is what is passed into Mutect2.…
  • But isn't parameter --minPruning the same as the one you mentioned? Setting up from the default of 2 to 5 has sped things up sixfold. ((Unless it was the other parameter --max-num-haplotypes-in-population which I also changed))
    in Mutect2 Comment by steveb January 2019
  • Okay. I am seeing that --orientationBias has not sped things up. However I am trying the two other suggested parametrs but Mutect2 does not have a --pruning-lod-threshold. And not sure if you meant instead one of: --minPruning 2 Minimum supp…
    in Mutect2 Comment by steveb January 2019
  • OKay good to know. The 'collect raw data' stage is complete and I have the 3 files from the output of CollectF1R2Counts. I am using them as inputs to LearnReadOrientationModel and waiting for output now. Hopefully running Mutect2 with the argum…
    in Mutect2 Comment by steveb January 2019
  • Returning after awhile...trying to create Oreintation Bias filter as in workflow presented by davidben above on this board. Please provide some clarificaton. You give the first two steps to use CollectF1R2Counts and LearnReadOrientationModel as i…
    in Mutect2 Comment by steveb January 2019
  • Continuing about FFPE and PanelOfNormal, would it be better to create a Panel with the loads of FFPE Tumour samples and treat it as a panelOfNormal? Or to use nothing at all? We generally do not have FFPE tumour lib.s. Still investigating --or…
    in Mutect2 Comment by steveb December 2018
  • Do you mean ? --orientation-bias-artifact-priors null table of prior artifact probabilities for the read orientation filter model
    in Mutect2 Comment by steveb December 2018
  • We want to try using MuTect2 on FFPE genomes. Should the panel of normals be made of up FFPE normals?
    in Mutect2 Comment by steveb November 2018
  • From previous posts I see that Spam Filters have disabled people from posting previously....So I will wait to contact somebody after NOv25 to verify my account and alllow me to post my quetion about creating PON for FFpe SAMPLES
  • is this affecting me? I cannot post a question to any forum!