1. Community
2. Somatic
3. gatk 4.1 vs 4.6 - increased number of low AF variants detected by mutect2

Hi Julia Belk There are certainly changes made to Mutect2 as versions progress and those changes are all for the betterment of the tool. Along these 2 versions here are some of the highlights that ...

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• Gökalp Çelik
• December 12, 2024 07:44
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1. Community
2. Germline
3. Hard filtering using using germline-resource

Hi Shashwat Sahay Germline resource is used as a prior for Mutect2 to decide whether there is enough suspicion for a site to be of germline origin. Germline Filter is explained more deeply in our d...

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• Gökalp Çelik
• December 11, 2024 18:52
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1. Community
2. Germline
3. Error in GnarlyGenotyper (QUALapproxkey)

Hi Gabriele Magris There is a paramter in ReblockGVCF tool to add that INFO field to reblocked GVCFs. The below parameter adds that field.  --do-qual-score-approximation true If you have not done s...

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• Gökalp Çelik
• December 11, 2024 18:32
• 0 votes

1. Tool Index
2. 4.1.4.1
3. Mutect2

Sure you can use it. 

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• Gökalp Çelik
• December 11, 2024 12:54
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1. Community
2. General Discussion
3. Joint calling with Mutect2 with mitochondria mode

Hi Le Qi Our mitochondria workflow does not include a joint calling flow therefore you may be on your own to devise a methodology. If you are only interested in generating a list of sites for futur...

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• Gökalp Çelik
• December 09, 2024 16:52
• 0 votes

1. Community
2. General Discussion
3. GATK GRCh38 Reference

Hi Yasir K Currently we do not support AWS platforms therefore we cannot help on the availability of resources within AWS. Our original hg38 contained all unlocalized contigs, alt contigs and HLA s...

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• Gökalp Çelik
• December 09, 2024 08:40
• 0 votes

1. Community
2. Documentation Questions
3. How do adapter sequences not contribute to alignment if the base quality is set to 2 with SamToFastq but BWA-MEM does not consider base quality scores?

Hi kescullator Adapter cleanup is more of a philosophical perspective rather than a hard written rule. Some prefer keeping adapter sequences albeit with low base call qualities to ensure they are n...

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• Gökalp Çelik
• December 09, 2024 08:34
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1. Community
2. Somatic
3. mutect2 results

Hi Liroz Hafouta NALOD annotation is better explained here in the document in our github repository. More of our annotations can be found in this document as well. https://github.com/broadinstitute...

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• Gökalp Çelik
• December 09, 2024 08:25
• Edited
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1. Community
2. Special GATK Use Cases
3. Mutect2 Calls for non-tumor pooled samples - no variants pass filters

Hi Ren Hamm Since you are using Mutect2 to call variants with allelic fractions in your pooled samples there is no need for adjusting ploidy for your samples. You might want to enable high sensitiv...

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• Gökalp Çelik
• December 09, 2024 07:58
• 0 votes

1. Technical Documentation
2. Glossary
3. Intervals and interval lists

You can checkout the masked dragen reference files from the bucket below https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0/dragen_reference   

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• Gökalp Çelik
• December 04, 2024 12:13
• 0 votes