David Benjamin
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Activity overview
Latest activity by David Benjamin-
David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
@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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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
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...
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David Benjamin commented,
TA The issue with the clustered events and haplotype filters when running in -genotype-germline-sites is a real problem. These filters should only be triggered by a cluster of technical artifacts ...