Robert Bremel
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Recent activity by Robert Bremel Sort by recent activity-
./gatk BuildBamIndex --INPUT fname.bam
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I had a similar?? issue crop up with BuildBamIndex in the docker 4.3.0.0 version on Windows 10 with WSL2 and DockerDesktop BuildBamIndex is supposed to only need a --INPUT argument. It runs and ...
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I have been using the GATK Docker image with Docker Desktop on a Windows workstation and it works fine. As a bit of a displacement activity while I am dodging delta I am thinking about building a ...
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Hi, I had a strange occurrence that seems to be a glitch in the system somewhere. A week or so ago I had something crop up with Funcotator which led me to install v1.7 of the source materials. I ...
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Hi, I copied it from the Funcotator webpage, Just to be clear -- I am running the Docker version in Docker Desktop on a Windows 10 workstation. The workstation has 128 GB memory and I believe Doc...
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Thanks again Genevieve, I think I have stashed the offending lines somewhere I will see if I can find them. It was a really unusual indel with three TLOD values each of which was mapping perhaps a...
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Thanks Genevieve, I will download and install the 1.7 data sources. I thought I was really up to date using 1.6 as 1.2 is in your examples. I found a workaround that I could remove two lines fro...
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Sorry, I really don't know about anything prior to 4.1.7.1 (only Docker). I am relatively new to this whole area having spent my career downstream in the protein world! :-) I only happened on ...
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I combined the funcotator.maf files and mutect2.vcf files from 20 variant sets and tallied-up the differences. I have only been working at this for a couple of months but the issue seems to arise i...
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I am using the docker version 4.1.8.1 vcf file ##source=FilterMutectCalls##source=Mutect2 -default command Funcotator --output mydata/P58772/analysis/P58772_7_mutect2_funcotator_hg38.maf -...