Genevieve Brandt (she/her)
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Activity overview
Latest activity by Genevieve Brandt (she/her)-
Genevieve Brandt (she/her) commented,
This is the best practices workflow page: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
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Genevieve Brandt (she/her) commented,
Thank you for your post, B! 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 detai...
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Genevieve Brandt (she/her) commented,
Thank you for your post, Franziska! 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 mo...
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Genevieve Brandt (she/her) commented,
Hi David Medina, Unfortunately, there isn't a better way to do this. The RMSMappingQuality annotations are annotated by the mapper and cannot be re-annotated in GATK if they are missing. Best, Gene...
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Genevieve Brandt (she/her) commented,
Hi Henri-Jean Garchon, I brought this issue up with the developers to see if they had any insight. We were wondering if you concatenated your GVCFs at all? And if you could check your bed file that...
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Genevieve Brandt (she/her) commented,
Hi LG, It has been a while since we've heard from you, so we'll be closing out this ticket in our system. However, please note that if you still require assistance, you need only respond to this th...
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Genevieve Brandt (she/her) commented,
Hi Benjamin Singer, It has been a while since we've heard from you, so we'll be closing out this ticket in our system. However, please note that if you still require assistance, you need only respo...
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Genevieve Brandt (she/her) commented,
Hi ulitskyi, I brought this up with our developer team to see if there was anything else we recommended for amplicon data. They recommended that you fully turned off the downsampler off by setting ...
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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...