Arun Seetharam
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Latest activity by Arun Seetharam
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Arun Seetharam commented,
Done!
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Arun Seetharam commented,
This was from another account. I've shared the workspace with the support, here are the details: 1. Link to the workspace: https://app.terra.bio/#workspaces/GATK_test_run_2022-07-01/GATK4-B73v5-tes...
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Arun Seetharam created a post,
processing-for-variant-discovery-gatk4 workflow: fails repeatedly at SamToFastqAndBwaMem step
Hello, I'm not sure if I'm doing something wrong, but I've been trying to test the GATK Best Practices Germline SNPs and INDELS with non-downsampled files, and it seems to have a problem at the BWA...
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Arun Seetharam commented,
Hi @Anika Das Thank you for pointing me in the right direction. I was able to find a version of joint genotyping identical to the one I used to run locally (simple bash script). If interested, th...
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Arun Seetharam created a post,
Running `GATK Best Practices Germline SNPs and INDELS` on custom genome
Hello, This question is related to `GATK Best Practices Germline SNPs and INDELS` workspace and my question is about implementing this on a custom genome (non-model) species. Our real dataset (~4...
- Arun Seetharam
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- 4 comments
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