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3. haplotycaller --alleles : arrayIndexOutofBoundsException

HI David, Version 4.5.0 resulted in the same error and fix.  Best,  Geert

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• Geert Vandeweyer
• January 15, 2024 12:31
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3. how to specify number of threads parameter in GATK Haplotpyecaller command line ??

Hi Nikhil, we've been using these settings to control threading in GATK 4+ (to some extend) : - Haplotypecaller takes the option :  --native-pair-hmm-threads 4- CNNScoreVariants : through an env va...

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• Geert Vandeweyer
• December 05, 2023 07:05
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3. Haplotypecaller 4.5.2.0 --alleles unexpected output

Thank you for looking into the problem ! 

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• Geert Vandeweyer
• April 02, 2022 11:03
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3. Haplotypecaller 4.5.2.0 --alleles unexpected output

Genevieve Brandt (she/her) : I've uploaded the data to the FPT client. Name == HaplotypeCaller.unknown_alleles.tar.gz There's one of the unexpected alleles called in the provided region.  Thanks fo...

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• Geert Vandeweyer
• March 18, 2022 12:35
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1. Community
2. Germline
3. Haplotypecaller 4.5.2.0 --alleles unexpected output

Yes, but I'll double check. If you can send me a private message, I can share the data. (Patient material)

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• Geert Vandeweyer
• March 16, 2022 10:48
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