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3. GenomicsDBImport: Attempting to genotype more than 50 alleles

Most likely the reason that you have so many genotypes as these sites is because the data is low quality there. With 37 samples, I wouldn't expect that high quality variant sites would have over 50...

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• Genevieve Brandt (she/her)
• August 10, 2022 01:43
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3. GenomicsDBImport: Attempting to genotype more than 50 alleles

Juan Pablo Aguilar Cabezas thank you for sharing! These are just warnings, not errors. Please see this forum post for more details: https://gatk.broadinstitute.org/hc/en-us/community/posts/36006103...

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• Genevieve Brandt (she/her)
• August 10, 2022 00:40
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3. "Could not determine local host name"

Hi Pryce Turner, Thank you for your help describing this strange behavior. The developers agree that we want to try to fix this, so I have a created a github ticket so that they can look into the i...

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• Genevieve Brandt (she/her)
• August 09, 2022 21:40
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3. low sequencing read depth on Y chromosome (ploidy=1)

Thanks Karen for the update here! We definitely want to find out why you might be seeing these results. First, I want to point you to this article regarding HaplotypeCaller's algorithm: Local re-as...

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• Genevieve Brandt (she/her)
• August 09, 2022 21:29
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3. GenomicsDBImport: Attempting to genotype more than 50 alleles

Juan Pablo Aguilar Cabezas could you share the warning/error message you are getting along with your GenotypeGVCFs command line and GATK version? 

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• Genevieve Brandt (she/her)
• August 09, 2022 21:06
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3. How to run docker gatk outside container

Thank you for your post, Kol Yan! 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)
• August 09, 2022 20:59
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3. FindBadGenomicKmersSpark running indefinitely

Hi Wei Yuan, Thank you for the update and giving more insight into your use case. Unfortunately, the GATK Spark SV pipeline is not maintained in favor of the much improved GATK-SV pipeline. The Spa...

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• Genevieve Brandt (she/her)
• August 04, 2022 19:42
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3. Find rate of homozygosity

Thank you for updating this post Joyce Anon! I'm sure this will be helpful for other GATK users in the future. 

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• Genevieve Brandt (she/her)
• August 04, 2022 19:28
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3. FindBadGenomicKmersSpark running indefinitely

Thanks Wei Yuan for trying that so quickly and getting back to us!  Could you also try adding the java -Xmx option to your command line to limit the amount of memory java uses?  Explanation about -...

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• Genevieve Brandt (she/her)
• August 03, 2022 19:10
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3. "Could not determine local host name"

Pryce Turner could you share the command line and log that you get with the docker image?

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• Genevieve Brandt (she/her)
• August 03, 2022 15:27
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