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Hi GATK Team, I'm trying to use RevertSam on a BAM file that is ~161GB in size and running into a "No space left on device error". The job storage was ~600GB GATK version: 4.5.0.0 Command: gatk --j...

• Lindo Nkambule
• February 07, 2024 20:13
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Hi GATK Team, I have ~350 BAM files that are about 150GB each in size. I have been using some of the GATK workflows as a reference but the SamToFastqAndBwaMemAndMba (mapping reads to reference) ste...

• Lindo Nkambule
• January 05, 2024 17:02
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Hi GATK Team, I'd like to know if it possible to restrict the output to within a specific interval? I am running ApplyVQSR and supplying an interval file with the interval chr1 111057913 117227796 ...

• Lindo Nkambule
• October 12, 2022 16:31
• Edited
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Hi GATK team and community, I've encountered an  java.util.ArrayList cannot be cast to java.lang.String error while trying to run VariantRecalibrator   GATK version used: 4.2.6.1 Exact command used...

• Lindo Nkambule
• August 29, 2022 20:14
• 2 followers
• 3 comments
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Hi GATK team and community, I've encountered an IndexOutOfBoundsException error while trying to run VariantRecalibrator GATK version used: 4.2.6.1 Exact command used: gatk --java-options -Xms{java_...

• Lindo Nkambule
• August 10, 2022 19:55
• Edited
• 3 followers
• 14 comments
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Hi, I am trying to merge a couple of GVCF files generated using HaplotypeCaller but getting Caused by: java.util.zip.ZipException: Not in GZIP format When I do the below command, the header seems o...

• Lindo Nkambule
• June 16, 2021 15:34
• 2 followers
• 1 comment
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