
Genevieve Brandt (she/her)
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Recent activity by Genevieve Brandt (she/her) Sort by recent activity-
This is the best practices workflow page: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
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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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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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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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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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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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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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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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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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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...