1. Community
2. Somatic
3. Mutect2 issue with --force-active: not all regions are active

Thanks for the update Maria and for providing these screenshots. I'm continuing to look into possible explanations. From the examples you chose, are there any specific coverage levels that you thin...

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• Genevieve Brandt (she/her)
• September 17, 2021 16:53
• 0 votes

1. Community
2. Germline
3. Error in merged bam files

Hi Priyadarshini Thirunavukkarasu, I think for this issue you will want to go back and re-do the steps that caused this issue to make sure there were not problems during those steps where mates wer...

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• Genevieve Brandt (she/her)
• September 15, 2021 18:53
• 0 votes

1. Community
2. Germline
3. In CNV Caling, why the intervals in two batches are not consistent?

Hi rq m, This output is from CollectReadCounts, correct? It looks like this is the expected behavior for this tool and I don't see any option for including intervals that have no coverage in the ou...

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• Genevieve Brandt (she/her)
• September 15, 2021 18:47
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1. Community
2. General Discussion
3. VariantFiltration MQRankSum error: "-12.5 is not a recognized option"

Thanks for the update Chloé Girard!

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• Genevieve Brandt (she/her)
• September 15, 2021 16:19
• 0 votes

1. Community
2. Somatic
3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Thanks Ruiqiao Bai! Could you run UpdateVCFSequenceDictionary to make sure that the dictionary of the lifted_small_exac_common_3.hg19.vcf.gz file is up to date?

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• Genevieve Brandt (she/her)
• September 15, 2021 16:17
• 0 votes

1. Community
2. Documentation Questions
3. Interpretation of gene_summary output from DepthofCoverage

Okay I see, thanks for sharing these updates! What version of GATK4 are you running?

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• Genevieve Brandt (she/her)
• September 15, 2021 16:14
• 0 votes

1. Community
2. Documentation Questions
3. Interpretation of gene_summary output from DepthofCoverage

Seunghun Han, it's not clear to me whether this is an issue with the GATK output or with the method you are using to view the file. Could you share a screenshot of what this output looks like on th...

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• Genevieve Brandt (she/her)
• September 14, 2021 16:32
• Edited
• 0 votes

1. Community
2. General Discussion
3. cfDNA targeted sequencing - analysis pipeline

Hi Anna, 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 forum ...

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• Genevieve Brandt (she/her)
• September 14, 2021 16:26
• 0 votes

1. Community
2. Documentation Questions
3. Mark duplicates in merged bam files sorted by coordinates

Hi Priyadarshini Thirunavukkarasu, I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Germline topic is for reporting bugs and issues with GATK. Yo...

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• Genevieve Brandt (she/her)
• September 14, 2021 16:23
• 0 votes

1. Community
2. Documentation Questions
3. How do I call somatic mitochondrial variants?

Hi Ruiqiao Bai, I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Somatic topic is for reporting bugs and issues with GATK. You can read more abou...

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• Genevieve Brandt (she/her)
• September 14, 2021 16:21
• 0 votes