
D B
- Total activity 21
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 3
- Subscriptions 4
Comments
Recent activity by D B Sort by recent activity-
I'm also observing a rather abnormally high number of indels with Mutect2, specifically insertions. When comparing to a group of previously generated VCF files using the same data a couple years ag...
-
Hey vctrymao, With regards to #4, David Benjamin has covered potential scenarios in one of the previous comments: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057810051/comments/3600...
-
Hey vctrymao, Aside from the HaplotypeCaller command that I mentioned in one of my comments, nothing else was run. Like you said, it is generally advised (GATK best practices) to run multiple sampl...
-
In case anyone was wondering if this is the case for other samples as well, I have tried with a couple of other matched data and saw similar numbers (10-15% overlap between tumor-only and matched n...
-
Hi David, Sorry to keep bothering you with all my questions. From my previous discussion with people from GDC, they use 4,000+ blood normal samples to create PoN using GATK4 (v4.0.4.0). Some inform...
-
How confident are calls retained using the option '--genotype-germline-sites' for the germline variants (since it is said to be experimental)? I've browsed through some older posts, but haven't bee...
-
Hi Beri, Just wanted to confirm that pulling from Github repo seemed to have resolved the issue. Is it correct to interpret the error message as: during the run, the current release version of MuTe...
-
Thanks Beri. I thought I might add the full error message as a reference for the dev team or whoever might find useful. The command I run generates a .VCF file, but if you look at it, MuTect2 seems...
-
Thank you! Will I be notified on this post or will I have to follow up in another manner?
-
I don't think that's true. Examining the log from the GATK run for the problematic chromosome, the arguments are correctly provided since I can observe the lines indicating that the file has been p...