D B
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Activity overview
Latest activity by D B-
D B commented,
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...
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D B commented,
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...
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D B commented,
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...
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D B commented,
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...
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D B commented,
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...
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D B created a post,
Mutect2 - somatic variant calling with/without matched normal sample
a) GATK version used v4.1.4.1 b) Exact GATK commands used Mutect2 w/ matching normal gatk Mutect2 -R hg38.fa \-I input_tumor.bam -I input_normal.bam \-tumor tumor_sample -normal normal_sample \-pon...
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D B commented,
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...
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D B created a post,
Filtering somatic calls from tumor-only variant calling
[GATK version used - v4.1.4.1] Hello, I have germline and somatic variants called using HaplotypeCaller and Mutect2. As you can see from the title of the posting, it was done using tumor samples wi...
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D B commented,
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...
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D B commented,
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...