1. Community
2. Non-Human
3. java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

Hi Zane Swaydan, I think I've found a related issue, which came up in GATK 4.2.4.0: https://github.com/broadinstitute/gatk/issues/7639 and has since been solved. Could you try creating your Genomic...

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• Genevieve Brandt (she/her)
• June 30, 2022 20:40
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1. Community
2. New User Advice
3. Mutect2 with and without UMI information

Hi Matthew Lueder, Yes, if your data has UMIs, the only step this will change is the MarkDuplicates step. You will need to perform UMI-aware read deduplication. I am not familiar with the other too...

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• Genevieve Brandt (she/her)
• June 29, 2022 22:05
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1. Community
2. General Discussion
3. Differentiating variant site from Force call or de novo

Hi Kevin Nathanael Ramanto, There's no option for this distinction. If a site is homozygous reference and force called, there was no variant at that site. Also, generally sites with a QUAL score lo...

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• Genevieve Brandt (she/her)
• June 29, 2022 21:43
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1. Community
2. General Discussion
3. CollectHsMetrics fold-80 value very high

Barbara Iadarola Leonardo Vincenzi thank you for your patience while we looked into this question. CollectHsMetrics filters for base quality 20 and mapping quality 20 as default. These parameters a...

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• Genevieve Brandt (she/her)
• June 29, 2022 21:19
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1. Community
2. General Discussion
3. Recommended tool for obtaining thresholded covered genomic regions

Hi Philipp Hähnel, There isn't a specific tool that can get this interval list for you. Your best bet would be to use DepthofCoverage and do some post processing.  Please let us know if you have an...

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• Genevieve Brandt (she/her)
• June 29, 2022 20:29
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1. Community
2. New User Advice
3. Variant Quality Score Recalibration

Hi Jakub S, Regarding SnpEff and functional annotations, VQSR doesn't use any functional annotations to make the model. You can use any annotations that you prefer. If you want all of the standard ...

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• Genevieve Brandt (she/her)
• June 29, 2022 20:27
• 0 votes

1. Community
2. General Discussion
3. Panel of normals for Mutect2 GRCmXX

Priyam Patel we now have an updated Panel of Normals workflow that is slightly different than  your comment. Please note it uses GenomicsDBImport and CreateSomaticPanelOfNormals instead of MergeVcfs.

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• Genevieve Brandt (she/her)
• June 29, 2022 20:08
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1. Community
2. Germline
3. Variant filtered from GVCF

Hi LP, I'm glad you are seeing improvement when using the --linked-de-bruijn-graph option! The -linked-de-bruijn-graph option is relatively new so our developers are still determining if they want ...

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• Genevieve Brandt (she/her)
• June 29, 2022 19:57
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1. Community
2. Special GATK Use Cases
3. Aligning very short reads

Hi EvanKristiansen, We would recommend that you use the older version of BWA (bwa aln), not BWA MEM if you have very short reads. MEM stands for minimum exact match, because the reads have to have ...

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• Genevieve Brandt (she/her)
• June 29, 2022 18:47
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1. Community
2. General Discussion
3. FastqToSam gives me wrong output for read pairs

Thanks for the update Bastiaan! Glad it's working.

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• Genevieve Brandt (she/her)
• June 23, 2022 15:40
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