Genevieve Brandt (she/her)
- Total activity 4351
- Last activity
- Member since
- Following 0 users
- Followed by 14 users
- Votes 24
- Subscriptions 1330
Comments
Recent activity by Genevieve Brandt (she/her) Sort by recent activity-
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. ...
-
Thanks for the update, Tanay! Glad it is working for you now!
-
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...
-
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...
-
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...
-
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...
-
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 ...
-
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....
-
Hi LOIC TALIGNANI, Thank you for writing into the GATK forum so that we can assist you with this question! I don't see any overt errors with your ValidateSamFile command, however, it does look lik...
-
Hi Tanay, Usually you would get the PU information from wherever your sample was sequenced. However, if you do not have the information, PU is not required by GATK so you do not need to include it....