Thomas Stevens
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Activity overview
Latest activity by Thomas Stevens-
Thomas Stevens commented,
Hi David, The reference does have the chr prefix as well. I left Funcotator running for around 5 days and it never progresses. GATK also never aborts it just stays stuck right at the beginning. F...
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Thomas Stevens created a post,
Funocator not moving along traversal
Hi, I'm trying to run the somatic variant calling pipeline. I've gotten to the funocator step but when I run funocator it never moves along the traversal. I'm not sure if the information its giving...
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Thomas Stevens commented,
Looking into this further, its more confusing. Both my variants and the data stored in funcotator_dataSources.v1.8.hg38.20230908s have the chr notation. Why is it searching for the non chr format?
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Thomas Stevens created a post,
Funocator chromosome missmatch to somatic variant calling pipeline
REQUIRED for all errors and issues: a) GATK version used: v4.5.0.0 b) Exact command used: gatk Funcotator -variant ../out/Filter_mutect/G1_2nM_BL_raw_variants.vcf \--reference /export/home/bin/gen...
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Thomas Stevens created a post,
AddOrReplaceReadGroups argument value query
Hi, I just wanted to ask for clarification on what exactly is important for GATK in picards AddOrReplaceReadGroups function. From reading other forums, it seems like the only important information...
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Thomas Stevens commented,
Thanks, I unfortunately can't currently use docker with the HPC system. But, I can try to find a solution to that if I can't fix the conda method.
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Thomas Stevens created a post,
GATK conda install issues
Hi, I'm having issues with installing gatk through conda on a HPC system. I originally installed gatk4 through https://anaconda.org/bioconda/gatk4 which worked fine until I got to the AnalyzeCovar...
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Thomas Stevens commented,
Hi Gökalp Çelik, Sorry, I feel like I'm missing something obvious but how do I know which of those files I should use. I've found alot of links talking about them but nothing clarifying why you sh...
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Thomas Stevens commented,
Hi Gökalp Çelik, Sorry to ask more questions but I forgot about the baserecalibration step and am stuggling to find examples that state what files should be used for this step as there seems to be ...
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Thomas Stevens commented,
Thank you. I wasn't certain if it was still appropriate to use the public files with this dataset so thanks for clarifying that.