1. Community
2. Documentation Questions
3. Germline sites in Mutect2

Hi , The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlo...

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• Bhanu Gandham
• March 21, 2021 04:21
• 0 votes

1. Community
2. Germline
3. GenomicsDBImport for the WGS sample gvcfs running too slow?How to fix it to achieve joint calling?

Hi Xiya Song   Please upgrade to latest version of GATK v4.2. The version you are using is a very old one. The latest version has many improvements that improve speed.   Also please take a look at ...

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• Bhanu Gandham
• March 15, 2021 18:39
• 0 votes

1. Community
2. Special GATK Use Cases
3. Question: Variant Calling when Genetic Distance between Reference and Samples is Greater than it is for Humans: Does GATK still perform well?

Hi , The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlo...

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• Bhanu Gandham
• March 15, 2021 18:34
• 0 votes

1. Community
2. Non-Human
3. Error: ValidateSamFile Value was put into PairInfoMap more than once.

Sounds like you are having issues with samtools and not GATK. I have not seen this error before so unfortunately can't help with this. I suggest to reaching out to the samtools support team or post...

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• Bhanu Gandham
• February 26, 2021 23:07
• 0 votes

1. Community
2. Other
3. BaseRecalibrator on MT .bam files

Sharon Cox If you see "Tool returned: SUCCESS" at the bottom of the log and you get an output, then the tool ran just fine. The progress meter is only giving you some info on what the tool encounte...

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• Bhanu Gandham
• February 26, 2021 23:00
• 0 votes

1. Community
2. Somatic
3. 1 year-old bug in libgkl that has not been fixed affecting FilterAlignmentArtifacts and HaplotypeCaller

Note: The solution for this query is being discussed in this github issue: https://github.com/broadinstitute/gatk/issues/5690

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• Bhanu Gandham
• February 23, 2021 00:07
• 0 votes

1. Community
2. Germline
3. VariantRecalibrator error the same name but different lengths, resources of GRCh37 or hg38?

Hi, The explanation for this issue has been provided on this forum multiple times. Please look through our forum threads for this error : https://gatk.broadinstitute.org/hc/en-us/articles/36005342...

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• Bhanu Gandham
• February 21, 2021 14:02
• 0 votes

1. Community
2. Somatic
3. mutect2 error: "Unknown file is malformed: Could not read sequence dictionary from given fasta file refereces.dict"

zdr j   With GATK you need to use the same reference for alignment and variant calling.  I used hg38 reference before, and then I faced this error: "Input files master sequence dictionary and read...

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• Bhanu Gandham
• February 16, 2021 16:08
• Edited
• 0 votes

1. Community
2. Non-Human
3. output stuck in GenotypeGVCFs

Hi tengMX I wonder if you are running out of memory. Can you confirm that you have enough memory left after processing the first 26 chromosomes?  Are you following the GATK best practices pipeline...

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• Bhanu Gandham
• February 13, 2021 13:32
• Edited
• 0 votes

1. Community
2. Germline
3. Mapping quality issue due to alternate contig for loci on Chromosome 17 in hg19 reference FASTA in the GATK Bundle; unable to force the variant to be called on HaplotypeCaller

Hi , The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlo...

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• Bhanu Gandham
• February 12, 2021 23:12
• 0 votes