Genevieve Brandt (she/her)
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Activity overview
Latest activity by Genevieve Brandt (she/her)-
Genevieve Brandt (she/her) commented,
Yes, that is the goal of the issue ticket I shared. They would like to understand why the current strategy of downsampling does not consistently work to call all variants with amplicon data. We don...
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Genevieve Brandt (she/her) commented,
Thanks Igor for the update. I did determine that this is a known issue with HaplotypeCaller: https://github.com/broadinstitute/gatk/issues/7567. However, there hasn't been much discussion on that i...
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Genevieve Brandt (she/her) commented,
Hi Henri-Jean, Thank you for writing into the GATK forum for this issue! It does seem like a strange error message, I haven't seen it before. What tool did you use to create these GVCFs? If it was ...
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Genevieve Brandt (she/her) commented,
Ok thank you, I am deleting the other post since it is a duplicate. We'll get back to you with a solution shortly!
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Genevieve Brandt (she/her) commented,
Hi Benjamin Singer, Thanks for writing into the forum with this issue! Most likely there was something wrong when you tried to install gatk. We don't maintain conda or bioconda so I can't determine...
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Genevieve Brandt (she/her) commented,
LG in the example you gave, both SM (sample names) are the same SM = 2. Could you clarify why you have two bam files with the same sample? You should merge these bam files before the Mutect2 step i...
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Genevieve Brandt (she/her) commented,
Tanay Biswas, is this other post the same issue? https://gatk.broadinstitute.org/hc/en-us/community/posts/10641300753819-GetPileupSummaries-malformed-header
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Genevieve Brandt (she/her) commented,
Thank you for your post, Joseph! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Germline topic is for r...
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Genevieve Brandt (she/her) commented,
Thank you for your post, Sushant! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more...
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Genevieve Brandt (she/her) commented,
Hi Tomás, We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up wh...