1. Community
2. General Discussion
3. CalculateContamination differs much in single and paired mode

Hi linouhao, To start with your original post, if you are doing tumor only vs matched normal calculations, it makes sense that you will get different values. Matched normal analysis is much more re...

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• Genevieve Brandt (she/her)
• January 25, 2022 03:30
• 0 votes

1. Community
2. Non-Human
3. gatk4-4.2.4.0-0 Fixmate Error

Hi Shazia Kunvar, This looks like an issue with your reads in the BAM file. I found some hits on google containing explanations and possible solutions. There's more out there too if you search htsj...

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• Genevieve Brandt (she/her)
• January 24, 2022 21:39
• 0 votes

1. Community
2. Other
3. --tmp-dir option user error

Thanks Karina for the update! That makes sense regarding the temp dir, I should have caught that. Glad you have it working!

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• Genevieve Brandt (she/her)
• January 24, 2022 21:26
• 0 votes

1. Community
2. Somatic
3. Mutect2 unexpected false negative due to changes in smith-waterman parameters?

Hi myourshaw, Thank you for your patience while we look into this difference you are seeing.  Can you verify that you are running the two GATK versions on the exact same input BAMs? Please take a ...

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• Genevieve Brandt (she/her)
• January 24, 2022 21:25
• 0 votes

1. Community
2. Other
3. GATK R plots with R v4.1.2

Hi Franz Gassner, Information about the R tool versions can be found in the tutorial (How to part I) Sensitively detect copy ratio alterations and allelic segments, in the section 'Tools Involved'....

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• Genevieve Brandt (she/her)
• January 24, 2022 20:23
• 1 vote

1. Community
2. Other
3. --tmp-dir option user error

Karina Martins try submitting your arguments like this: gatk --java-options "-Xmx16G" MergeBamAlignment \--ALIGNED_BAM "${local_out2}/${file}.aligned.bam" \--UNMAPPED_BAM "${local_out2}/${file}.unm...

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• Genevieve Brandt (she/her)
• January 24, 2022 18:01
• 0 votes

1. Community
2. General Discussion
3. pooled experiment means

Yes, that's correct! 

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• Genevieve Brandt (she/her)
• January 24, 2022 17:49
• 0 votes

1. Community
2. General Discussion
3. Somatic Hotspot mutation is filtered although evident with IGV

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

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• Genevieve Brandt (she/her)
• January 24, 2022 17:41
• 0 votes

1. Community
2. Non-Human
3. GenotypeGVCFs stalls while using --all-sites

Andrius Jonas Dagilis it doesn't look like there is going to be a quick solution for the GenotypeGVCFs bug. For the stalling issue, can you try running GenotypeGVCFs 4.2.4.0 with your GenomicsDB fr...

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• Genevieve Brandt (she/her)
• January 21, 2022 17:37
• 0 votes

1. Community
2. Documentation Questions
3. GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites

Oh good I'm glad to hear that you have it working now! Thanks for writing in so we could get GATK working for you!

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• Genevieve Brandt (she/her)
• January 21, 2022 16:13
• 0 votes