1. Community
2. Somatic
3. Mutect2 not calling a 4-bp deletion in BRCA1 with 50% AF

Hi, Based on the screenshots it is possible that this issue is the same as described in this issue ticket: https://github.com/broadinstitute/gatk/pull/6113.  As for disabling tool default read filt...

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• Bhanu Gandham
• April 03, 2020 17:55
• 2 votes

1. Community
2. Other
3. HaplotypeCaller -ERC GVCF -variant_index_type LINEAR

Hi Matilde   You are using a very old version of GATK which we do not support anymore. Please upgrade to the latest version of GATK v 4.1.9.0. The latest version of GATK does not require "-variant_...

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• Bhanu Gandham
• January 22, 2021 22:11
• 1 vote

1. Community
2. Other
3. Error in SplitNCigarReads

Hi Giulia Corsi   Can you please provide us with the  a runnable test case that reproduces the SplitNCigarReads issue? Once we have that, we can debug.

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• Bhanu Gandham
• August 31, 2020 18:42
• 1 vote

1. Community
2. Germline
3. GATK 4.1.7.0 VariantAnnotator Processing Speed Drop

That's great! And thanks for the update Louis Bergelson   And thank you danilovkiri for bringing this to our attention!

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• Bhanu Gandham
• June 23, 2020 15:21
• 1 vote

1. Community
2. Non-Human
3. GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0

Hi ABours   We looked into it and we don't think this is necessarily an unwanted behaviour. This call is trying to tell us that something is going on in this region. You can see that the PL values ...

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• Bhanu Gandham
• June 17, 2020 04:41
• Edited
• 1 vote

1. Community
2. Germline
3. GATK 4.1.7.0 does not annotate ID using dbSNP build 153 VCF

Hi danilovkiri   We are looking into fixing this. Will share a PR with you for it soon. Stay tuned!

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• Bhanu Gandham
• May 29, 2020 16:44
• 1 vote

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

Thank you for your response and contribution to building GATK knowledge-base in this forum Marley Yeong!  annabeldekker we haven't found a solution for this yet. When you do try this workaround ple...

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• Bhanu Gandham
• May 28, 2020 19:10
• 1 vote

1. Community
2. Germline
3. Cannot lock consolidation filelock; Cannot lock.

Can you try setting this environment variable and see if that solves the issue?   export TILEDB_DISABLE_FILE_LOCKING=1

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• Bhanu Gandham
• May 28, 2020 16:59
• 0 votes

1. Community
2. Germline
3. Not getting vcf file

Hi,   We see this error when your bam file fails tag requirements. Run ValidateSamFile on your bam/sam file. Also take a look this doc which describes how to resolve issues with sam/bam file: mhttp...

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• Bhanu Gandham
• May 15, 2020 17:18
• 1 vote

1. Community
2. Other
3. Do I need to perform fastqc and adapters trimming before gatk pipeline?

Hi danilovkiri   Thank you for jumping in and helping the GATK community. We appreciate your contribution!

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• Bhanu Gandham
• May 10, 2020 23:57
• 1 vote