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3. libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow

Thank you for posting the solution Marta Giovalli!

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• Genevieve Brandt (she/her)
• September 26, 2022 18:03
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1. Community
2. General Discussion
3. java.lang.IllegalArgumentException: Invalid interval in FuncotateSegments

Thanks tc for your insight about how you worked around this issue! Adel S it looks like it was you who commented on the github thread? The extra information that more users are seeing this will def...

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• Genevieve Brandt (she/her)
• September 24, 2022 00:34
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1. Community
2. General Discussion
3. CombineGVCFs - A USER ERROR has occurred: Bad input: Raw value for annotation has 1 values, expected 2

Hi David Medina, Do you know how these VCFs were created? It looks like there is an issue in your RMSMappingQuality annotation.  Best, Genevieve

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• Genevieve Brandt (she/her)
• September 24, 2022 00:29
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2. General Discussion
3. Fatal error detected by the Java Runtime Environment when running MarkDuplicates

Thank you Eduardo Maury, this is great news! I am so glad that both of the samples are now past the MarkDuplicates step. For the sample that failed SortSam, could you try with the recommendations i...

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• Genevieve Brandt (she/her)
• September 24, 2022 00:26
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1. Community
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3. Import gVCF to genomicsdb in parallel

Thank you for your post, Emyr James! 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 m...

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• Genevieve Brandt (she/her)
• September 24, 2022 00:14
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1. Community
2. Special GATK Use Cases
3. Can I swap the identities of the tumour and the normal samples to reverse verify the authenticity of the detected variants?

Thank you for your post, Di Pan! 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)
• September 23, 2022 23:47
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1. Community
2. Other
3. How can I build the GATK jar so that the intel native libraries are available?

Hi Mark Schreiber, Could you clarify what you mean by the official GATK jar? If I use the same command with the official GATK jar I don't get this warning and AVX is used. Thank you, Genevieve

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• Genevieve Brandt (she/her)
• September 22, 2022 23:08
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1. Community
2. General Discussion
3. Mutect2 low allele fraction mutation calling

Thank you for your post, TA! 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 Somatic topic is for report...

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• Genevieve Brandt (she/her)
• September 22, 2022 23:05
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2. General Discussion
3. Failure working with the tmp directory /tmp/

Hi Marta, 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...

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• Genevieve Brandt (she/her)
• September 22, 2022 23:02
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1. Community
2. Somatic
3. Picard error (AddOrReplaceReadGroups)

Hi Hyesun Cho, There is a tool that can help you to diagnose any issues with your sam file, called ValidateSamFile. Please take a look at this article for more details: https://gatk.broadinstitute....

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• Genevieve Brandt (she/her)
• September 20, 2022 23:57
• 0 votes