1. Community
2. Other
3. ValidateSamFile behavior

Hi Robert Edgar   Apologies. You mentioned GATK2 which got me confused. Anyway, you are using is Picard v2 so that's fine.  Now lets answer your questions: Yes you can provide a reference fasta us...

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• Bhanu Gandham
• March 02, 2020 20:23
• 1 vote

1. Community
2. Other
3. Loss of data after HaplotypeCaller

Thank you for your input SkyWarrior.   mbesskd5 In addition to that, also take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035891111-Expected-variant-at-a-specific-site...

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• Bhanu Gandham
• February 15, 2020 21:59
• Edited
• 1 vote

1. Community
2. Somatic
3. Can't use GATK or Picard's LiftoverVcf tool without encountering output format exception

Hi,    It looks like you provided a txt file in the REJECT argument, which should be a vcf file. Try REJECT=rejectedRecords.vcf

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• Bhanu Gandham
• February 07, 2020 19:25
• 1 vote

1. Community
2. Germline
3. GATK Funcotator and GATK VariantFiltration

Hi Amit Yes - the user will need to specify the `--exclude-field` option for each field they want to exclude from the output.  For instance, if they don't want the  Gencode_19_ncbiBuild field incl...

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• Bhanu Gandham
• February 06, 2020 20:36
• 1 vote

1. Community
2. Germline
3. MergeBamAlignment Error: "String tag does not have length() == 2: Cross-species contamination | CO"

Hi Shyam Sundar   This is a bug in the code and we are in the process of fixing it. You can follow the progress on it here: https://github.com/broadinstitute/picard/pull/1461   In the meantime, a w...

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• Bhanu Gandham
• February 03, 2020 21:55
• 1 vote

1. Community
2. Germline
3. Haplotypecaller usage (version decrepancy)

Hi stella   Since we do not support GATKv3 anymore I am not going to be able to provide a recommendation on results from GATKv3 tools. We recommend upgrading to GATKv4.

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• Bhanu Gandham
• January 31, 2020 13:58
• 1 vote

1. Community
2. Special GATK Use Cases
3. Trio Denovo annotation using VariantAnnotator PossibleDenovo not working?

Hi Jan, I apologize for the delay in getting back to you. I was attending a conference. Can you please try the latest version of GATK which is v4.2.2.0. The version you are using is quite old at th...

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• Bhanu Gandham
• September 11, 2021 17:22
• Edited
• 0 votes

1. Community
2. General Discussion
3. HRun not found in vcf header or INFO

Hi Mingzhou Fu, I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK. You can read more about ou...

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• Bhanu Gandham
• August 30, 2021 17:56
• 0 votes

1. Community
2. Germline
3. genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file

Hi Diya, Please post the exact command you are using, the version of the tool and the entire error log. 

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• Bhanu Gandham
• August 07, 2021 01:59
• 0 votes

1. Community
2. General Discussion
3. MuTect2 Phasing tags (PGT:PID:PS:) in FORMAT column: How to avoid/remove them?

Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as this topic is for reporting bugs with GATK. You can read more about our forum guidelines and the top...

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• Bhanu Gandham
• June 25, 2021 03:49
• 0 votes