Genevieve Brandt (she/her)
- Total activity 2126
- Last activity
- Member since
- Following 0 users
- Followed by 1 user
- Votes 17
- Subscriptions 691
Activity overview
Latest activity by Genevieve Brandt (she/her)-
Genevieve Brandt (she/her) commented,
Hi David Jaspez, We were able to confirm on our end that this looks like a bug. We're continuing to look into why this is happening and if there is a workaround, I'll hopefully get back to you next...
-
Genevieve Brandt (she/her) commented,
Hi Tracy Chew, Haha I've gotten the hang of spotting GATK's gripes :) I think that Data Pre-Processing for Multiplexed samples document has the steps you want to follow. It looks like the stand alo...
-
Genevieve Brandt (she/her) commented,
Rebecca Birnbaum, Hmmm, are you sure? In your stack trace in the post, the arguments for --allosomal-contig are as follows: --allosomal-contig chrX --allosomal-contig chrY Could you re-run this com...
-
Genevieve Brandt (she/her) commented,
Hi Rebecca Birnbaum, Is the command you gave from the same run of your error log? I don't see the --allosomal-contig argument in the command line: gatk PostprocessGermlineCNVCalls --model-shard-pat...
-
Genevieve Brandt (she/her) commented,
Hi William, The --alleles option is still available in GATK 4.2.0.0. If you only want those positions included, you can use the intervals option with -L which also accepts a VCF input. Let me know ...
-
Genevieve Brandt (she/her) commented,
Hi Ying! Glad you found what you were looking for, thanks for posting your solution. Genevieve
-
Genevieve Brandt (she/her) commented,
Hi jhy, I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK. You can read more about our forum g...
-
Genevieve Brandt (she/her) commented,
Hi David Jaspez, Thanks for posting here! We'll try to get it sorted out. Could you post your entire stack trace with this java option: --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' ? I...
-
Genevieve Brandt (she/her) commented,
Hi Tracy Chew, It looks like there are multiple read groups in your file but there is only one in the header. For example, ID: D0CC8ACXX.3_NA12877_S1_L003_1. You'll need to fix this issue in your b...
-
Genevieve Brandt (she/her) commented,
Hi Saskia, We are wrapping up the fix for this issue with the error message but we have not been able to replicate the error message you were getting. Would you be able to upload test data that cre...