Genevieve Brandt (she/her)
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suzy_bunters & Alia Parveen, Read groups are necessary for using GATK, you may just need to add them to your file. Usually read groups are added during alignment, but you can add them to your BAM w...
Hi Nils Homer, I have looked into both of your requests, and unfortunately right now it is not possible to increase the number of alleles supported in GenomicsDB import. One option you might try is...
Hi Yuna Son, you may have a problem with your read groups, and have named different samples as "Sample". This does not work for GATK because different samples need to be named accordingly. Please s...
Hi New_gatk_user, there is an issue with one of your files, at contig004333. It has the stop position at 0 and the start at 1, which will throw an error with GATK. You will need to fix this issue s...
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. ...
Hi Kresnodityo Jatiputro Widianto, Thank you for posting this question on the forum and for your patience for us to get a chance to take a closer look at your question. We (the support team) can de...
Hi Ranjan J. Sarma, Thank you for posting on the forum! One of our developers solved this issue here: https://gatk.broadinstitute.org/hc/en-us/community/posts/360071895952-Mutect2-s-support-for-MNP...
Thanks for your post igor! This has been fixed: https://github.com/broadinstitute/gsalib/releases/tag/2.2.1
Hi Mohammad Deen Hayatu, If GATK is having a hard time finding the dictionary, I would recommend using GATK to create an updated sequence dictionary and then trying to run the tool again. You can ...
Hi Jakub Savara, We took at the code and verified that it is fine to run SamToFastq on a coordinate or name sorted bam. There might be a slight performance benefit to run the tool with a name sorte...