
Robert Bremel
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Activity overview
Latest activity by Robert Bremel-
Robert Bremel commented,
./gatk BuildBamIndex --INPUT fname.bam
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Robert Bremel created a post,
BuildBamIndex
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Have run this script many times previously but problem occurred with the 4.3.0 update After ...
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Robert Bremel commented,
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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Robert Bremel commented,
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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Robert Bremel created a post,
Funcotator missing cDNA, Codon, and Protein Change for some chromosomes
AnsweredI am using the :latest docker version of GATK, running on Docker Desktop on a high-end Windows 10 workstation with 128GB RAM I had a strange occurrence that seems to be a glitch in the system so...
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Robert Bremel commented,
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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Robert Bremel commented,
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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Robert Bremel commented,
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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Robert Bremel commented,
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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Robert Bremel created a post,
Mysterious Funcotator issue
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: Docker 4.2.0 b) Exact command used: ./gatk Funcotator -R mydata/refs/Homo_sapiens_assembly38.fasta -V mydata/PAAD_00034_...