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3. GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases

Hi Genevieve, I understood. Thank you for your kind help! Best, HT  

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• HT
• October 10, 2021 11:08
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1. Community
2. New User Advice
3. GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases

Hi Genevieve, Thank you for your speedy reply! Noted that it was a bug in old versions. I followed the GATK best practice workflow and used HaplotypeCaller to create gVCF files. Then combined indiv...

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• HT
• October 02, 2021 04:39
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3. GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray

Hi Pamela, OK, I see. The latest workflow is indeed a better choice. Thank you again for your kind help! Best, HT

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• HT
• September 08, 2021 07:49
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1. Community
2. Special GATK Use Cases
3. GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray

Hi Pamela, Understood, I should always use the same version of GATK. Thank you for your suggestions! They are really helpful! Could you please help to submit a Github ticket? I would indeed like to...

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• HT
• August 27, 2021 16:11
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1. Community
2. Special GATK Use Cases
3. GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray

Hi Pamela, Thanks for your quick reply! I reindexing the fast file using samtools as you suggested. Now it works with GenotypeGVCFs in GTAK version 4.2.1.0 using old fasta data. I was wondering whi...

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• HT
• August 26, 2021 01:57
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