David Benjamin
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Recent activity by David Benjamin Sort by recent activity-
Jeffcgen2000 Different patients should not be combined in a single Mutect2 command. The correct command for patient1 would be: gatk Mutect2 \ -R reference.fa \ -I tumor1_patient1.bam \ ...
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Привет, Дмитрий, есть конкретная ситуация, которая тебя интересует? Что касается MNPs, используйте опцию `--max-mnp-distance`. Когда это Ноль, GATK считает их независимыми SNPs.
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Alexandre Mondaini That WDL file is misleading. It invokes multiple independent runs of Mutect2 on tumor-normal pairs, and each pair has a single tumor and normal. Given that Mutect2 should be ru...
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Hi Alexandre Mondaini, You should run Mutect2 in multi-sample mode, separately for each patient. That is: gatk Mutect2 -I normal1.bam -I tumor1.bam -I tumor2.bam -I tumor3.bam -normal normal1 . . ...
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@Ce Wang The change in 4.2.0.0 that had the effect you saw was this PR: https://github.com/broadinstitute/gatk/pull/6823. This fixed a bug where various read transformations were not actually havi...
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Hi Elisabetta Manduchi, I'm not aware of anything to point you to for using alt contigs to call somatic variants in the HLA, but a good method along the lines of your first approach is the Polysolv...
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ElenaGrassi I am trying to reproduce the error and it looks like it might already be fixed in the most recent version of the GATK. The 6 pairs you found were all PASS. Could you re-run with versi...
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TA The PON blacklists sites. Any variant allele at a PON site is rejected. This is intentional (although it is not always correct and can lead to false negatives) because often sites do have a ge...
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Joe Doasi You may also use multisample mode with a time series. The important thing is that all samples must come from the same person: multiple sites of one tumor, time series, primary tumor and ...
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G E Turning on -genotype-gemline-sites should not affect downstream filtering, but unfortunately I neglected to exclude germline sites from the clustered events filter, and so turning on this argum...