1. Community
2. Non-Human
3. empty variant to table file

  By default, the tool only extracts PASS or . (unfiltered) variants in the VCF file. Filtered variants may be included in the output by adding the --show-filtered flag. Take a look at the tool do...

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• Bhanu Gandham
• April 12, 2020 20:02
• 1 vote

1. Community
2. Other
3. GATK/Picard does not detect mates in paired-end BAM

Hi,   Take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035891231

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• Bhanu Gandham
• April 07, 2020 14:27
• 1 vote

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

Hi, How much physical memory do you have in addition to 50G? Is the data remote? Can you please share contents of '--sample-name-map samples.block0.map' file? You have few enough samples so maybe ...

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• Bhanu Gandham
• April 06, 2020 17:53
• 1 vote

1. Community
2. Somatic
3. Combining gVCFs containing MNPs is not supported for Ploidy Samples

Hi Lauren Audi   Checkout the new GATKv4.1.6.0 with this fix here: https://github.com/broadinstitute/gatk/releases/tag/4.1.6.0

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• Bhanu Gandham
• April 01, 2020 18:48
• 1 vote

1. Community
2. Special GATK Use Cases
3. GATK4 CNV calling in Wheat WES data very sensitive to small changes in minimum-mappability in FilterIntervals

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 27, 2020 15:17
• 1 vote

1. Community
2. Somatic
3. Combining gVCFs containing MNPs is not supported for Ploidy Samples

Hi Lauren Audi   This is a known bug in the code and it will be fixed in the next GATK release coming in the next couple of days. You can follow the progress on this issue here: https://github.com/...

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• Bhanu Gandham
• March 24, 2020 01:33
• 1 vote

1. Community
2. Germline
3. An error in GenotypeGVCFs

Hi Li Shanshan   I recommend you use HaplotypeCaller (GATK4.1) to regenerate the gVCF file. As suggested in the error there may be differences in how newer GATK versions calculate DP and MQ and hen...

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• Bhanu Gandham
• March 24, 2020 01:26
• 1 vote

1. Community
2. Germline
3. Less samples than expected due to malformed VCF

Hi sp580   You are using a very old version of GATK. Please upgrade to the latest v4.1.5.0 which has many of these issues fixed and try again and let us know if the issue persists.

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• Bhanu Gandham
• March 18, 2020 23:04
• 1 vote

1. Community
2. Germline
3. MarkDuplicatesSpark consumes enormous amount of RAM

Hi Yangyxt   The reason you are probably facing this issue is because you have not limit memory usage with `-xmx` argument or worker threads(which is possibly causing the use of all the cores) usin...

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• Bhanu Gandham
• March 16, 2020 18:44
• 1 vote

1. Community
2. Somatic
3. Segmentation fault when using GenomicsDBImport to create a panel of normals

Hi zohreh Fattahi   1. Yes. 2. Yes.

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• Bhanu Gandham
• March 13, 2020 18:08
• 1 vote