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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...

• Thomas Stevens
• March 25, 2024 11:12
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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...

• Thomas Stevens
• March 25, 2024 09:10
• Edited
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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...

• Thomas Stevens
• February 23, 2024 16:20
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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...

• Thomas Stevens
• February 23, 2024 13:51
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Hi, I'm trying to identify somatic mutations in treated MOLM-13 cell lines but I'm not certain about how I should produce one of the files required as input to the commands.  I found you can genera...

• Thomas Stevens
• February 20, 2024 10:17
• 2 followers
• 6 comments
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