David Benjamin
- Total activity 404
- Last activity
- Member since
- Following 0 users
- Followed by 1 user
- Votes 2
- Subscriptions 142
Activity overview
Latest activity by David Benjamin-
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...
-
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...
-
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...
-
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...
-
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 ...
-
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...
-
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 ...
-
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...
-
David Benjamin commented,
D the -normal argument specifies the normal samples; all others are presumed to be tumor samples.
-
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...