Genevieve Brandt (she/her)
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Activity overview
Latest activity by Genevieve Brandt (she/her)-
Genevieve Brandt (she/her) commented,
Hi ulitskyi, I noticed that you already uploaded data. We require that you wait until a support team member asks you before you upload data. With that being said, I am wondering what happens when y...
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Genevieve Brandt (she/her) commented,
Hi DHWANI DHOLAKIA, Thank you for writing into the forum with your question and your patience while we got back to you. Yes, you can run GATK on Ion torrent data. Unfortunately, we are not experts ...
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Genevieve Brandt (she/her) commented,
Hi Bob Ye Lindo Nkambule, Thanks for writing into the forum with this issue! Hopefully we can help out and we can get this resolved for you. You're right that the underscores are causing an issue. ...
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Genevieve Brandt (she/her) commented,
Thanks for the update, Tanay! Glad it is working for you now!
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Genevieve Brandt (she/her) commented,
Was the job paused at 36 hours? Or was it in the middle of the run? You can share your program log and I can take a look to see if there were any issues. If it never started (like the program log y...
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Genevieve Brandt (she/her) commented,
Well, these are errors with your bam file, so I think the snakemate pipeline is incorrectly deleting the text file. (ERROR::MISSING_PLATFORM_VALUE:Read name ERR3343471, A platform (PL) attribute w...
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Genevieve Brandt (she/her) commented,
Yes, it looks like these errors you got by running it in bash are helpful enough to determine what you need in your file. Glad it is working! If you're not familiar with read groups, take a look at...
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Genevieve Brandt (she/her) commented,
Great to hear that it's working! And yes, GenomicsDBImport can be a time consuming step. We put together an article with all of our performance recommendations here: GenomicsDBImport usage and perf...
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Genevieve Brandt (she/her) commented,
You should be able to run Mutect2 without the PU read group. I don't know about why your file size is different, I don't have enough information to determine. If you share the complete stack trace ...
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Genevieve Brandt (she/her) commented,
Hi Tomás Rodríguez, Thank you for writing into the GATK forum so that we can help you with this question! The good news is I think the reason your first command has an error is with a simple typo....