David Benjamin
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Latest activity by David Benjamin-
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 ...
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David Benjamin commented,
Alessio Locallo My question is: should I use the PON when I run Mutect2 in multi-sample as well? Or is the PON not necessary when running Mutect2 in multi-sample mode? You should still use a pa...
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David Benjamin commented,
D the -normal argument specifies the normal samples; all others are presumed to be tumor samples.
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David Benjamin commented,
Before answering your questions, we need to point out a few things: The panel of normals' role is only to clean technical artifacts, not remove germline mutations, which is handled by the germline...
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David Benjamin commented,
You have to specify -normal to tell Mutect2 which sample is the normal. You may exclude -tumor-sample.
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David Benjamin commented,
Just -normal-sample, and keep your other arguments the same. And you can continue to specify -tumor-sample if it's a hassle to change all your scripts, but it has no effect.
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David Benjamin commented,
TMB You are inadvertently running in multi-sample mode: Mutect2 thinks both samples are tumors. You need to specify -normal-sample, and -tumor-sample is a deprecated optional argument (it does not...