1. Community
2. General Discussion
3. Some problems in VCF filtering after GATK HaplotypeCaller step？

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
• May 10, 2020 23:48
• 1 vote

1. Community
2. Somatic
3. HaplotypeCaller fails with Exit code 3, but no further information is given

Another thing to try is validate your input BAM files with ValidateSamFile 

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• Bhanu Gandham
• April 30, 2020 02:36
• 1 vote

1. Community
2. Somatic
3. HaplotypeCaller fails with Exit code 3, but no further information is given

Looks like HaplotypeCaller is unable to read the input file. Try to run `samtools view -H <inputbam>` and see if that works. If that doesn't work either then it is not a GATK issue and you need to ...

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• Bhanu Gandham
• April 30, 2020 02:35
• 1 vote

1. Community
2. Other
3. Broken: conda env create -n gatk -f gatkcondaenv.yml

Hi,   Our conda env has not been tested for portability. We only guarantee that it will work on whatever version of Ubuntu is used in the Docker image and on Travis. However, since your request, we...

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• Bhanu Gandham
• April 30, 2020 02:25
• 1 vote

1. Community
2. Somatic
3. GATK doesn't find the MuTect2 tool?

Nicola Dick   What you are looking at is a very old version of GATK. Please look at the latest version which has the correct usage examples: https://gatk.broadinstitute.org/hc/en-us/articles/360042...

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• Bhanu Gandham
• April 30, 2020 02:14
• 1 vote

1. Community
2. Other
3. Posts pending approval now for 1 month

Hi mack812 I have released your posts.

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• Bhanu Gandham
• April 29, 2020 15:31
• 1 vote

1. Community
2. Germline
3. funcotator: dbSNP fields are empty

Hi Eugene Albert   We are creating a new funcotator resource soon and that should resolve this issue. You can follow progress on this here: https://github.com/broadinstitute/gatk/issues/6564

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• Bhanu Gandham
• April 22, 2020 15:38
• 1 vote

1. Community
2. Germline
3. FindBadGenomicKmersSpark not running

Hi Thanh Nguyen Nguyen   GATK only supports Java 8 and not Java 11. Please use java 8 and try again.

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• Bhanu Gandham
• April 15, 2020 16:09
• 1 vote

1. Community
2. Non-Human
3. GenomicsDBImport very slow on genome with many contigs

Hi Marley Yeong   I am very interested in how the workaround( pasting the contigs together) works out for you. Please share your experience after you have tested it. I wonder if the coordinates mi...

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• Bhanu Gandham
• April 13, 2020 19:27
• 1 vote

1. Community
2. Germline
3. GenomicsDBImport stuck on importing

Thank you for sharing your experience sp580 and helping us enrich the GATK-Community knowledge-base.

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• Bhanu Gandham
• April 13, 2020 16:30
• 1 vote