Philipp Hahnel
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Recent activity by Philipp Hahnel
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Thanks, Jason. The ultimate goal is to set up a proper multisample mutect2 pipeline. GATK currently does "multisample" by just running M2 in single tumor-normal pair mode for all pairs ... . Input ...
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Thanks, Jason! I'll take a look.
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That's a good point. Looking at the Mutect2 WDL, one of the tasks is CramToBam, which uses samtools, and does not make localization optional. Do you know where I can look into how GATK streams fil...
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Hi Jason, thanks a lot for spotting this embarrassing bug! I'm curious to hear your verdict on the fasta file too! Best, Philipp
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I gave you full access to the WDL
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All right, in the interest of time, I've re-created the testing workspace without authorization domain. https://app.terra.bio/#workspaces/carterlabtest/test Let me know if you can't access it!
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My PI is admin of that group. He'll do that as soon as he can.
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Hi Jason, thanks for coming back to me! I've shared the workspace with the email. The link is https://app.terra.bio/#workspaces/carterlabtest/test_mpileup I've set up this workspace to exactly show...
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Thanks for the response, Emil! I've uploaded a TSV which turned a supposed array into "['path1.bam', 'path2.bam']". I've meanwhile found this post https://support.terra.bio/hc/en-us/community/posts...
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Hi, I wanted to push this question again. I have the same problem, just for a table with hundreds of rows for which it is unfeasible to do said method by hand. Tar-ing the files doesn't make sense ...
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