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3. java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

Hi Anthony Dias-Ciarla, Link received, thank you! Let me know if you need more information about this issue!  Best, Zane

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• Zane Swaydan
• August 05, 2022 02:32
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1. Community
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3. java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

Hi Anthony Dias-Ciarla, Thank you for your explanation and your team for working hard on this!  I'm working on extracting intervals in "--force-output-intervals" with padding regions as separate "p...

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• Zane Swaydan
• August 04, 2022 08:29
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1. Community
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3. java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

Hi Anthony Dias-Ciarla, Thank you for your suggestion! I did some further tests and still have some problems here. When I use "--max-genotype-count 200 --genomicsdb-max-alternate-alleles 1201 --ma...

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• Zane Swaydan
• July 22, 2022 02:58
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1. Community
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3. java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

Hi Genevieve， Thank you for your prompt reply! I actually changed the GenomicsDBImport version to 4.2.6.1 for a test just after the post. Here I got the logs. Unfortunately, this still does not wor...

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• Zane Swaydan
• July 01, 2022 00:46
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