1. Technical Documentation
2. Glossary
3. VCF - Variant Call Format

As Loren Cassin Sackett has mentioned, it would be useful to have a further explanation. If it is not advised to combine VCFs for multiple samples, what would be the recommended method to compare v...

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• ISmolicz
• March 04, 2021 17:20
• 2 votes

1. Community
2. General Discussion
3. disabling NotDuplicateReadFilter in Mutect2

Hi jungmin choi, There are arguments that you can apply with Mutect2 (and other GATK tools) to either disable specific read filters (--disable-read-filter) or all default read filters (--disable-to...

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• ISmolicz
• April 06, 2021 16:36
• 1 vote

1. Community
2. Other
3. IlluminaBasecallsToSam: How do I specify one unique RGID per output uBAM?

Thank you for your reply Yossi Farjoun - your explanation is helpful. Just to confirm, following IlluminaBasecallsToSam (Picard), the uBAMs and downstream files per read group prior to merging shou...

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• ISmolicz
• November 16, 2020 10:39
• 1 vote

1. Community
2. Documentation Questions
3. What argument(s) should be used instead of --debug-graph-transformations?

Thank you for your reply David Benjamin. Apologies, I did not realise it was still an existing argument as it was not listed in the Mutect2 documentation argument list. My colleague ran the command...

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• ISmolicz
• June 13, 2023 10:04
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

Thank you for your reply David Benjamin. To clarify my above question, are there any other arguments in this troubleshooting document that should be set to true from the outset when using Mutect2 n...

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• ISmolicz
• April 26, 2023 14:05
• 0 votes

1. Community
2. Somatic
3. Missing mutations

Hi David Benjamin, Thank you for your reply. The functions of the arguments --genotype-germline-sites and --genotype-pon-sites are described with similar terminology in the Mutect2 documentation. H...

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• ISmolicz
• April 26, 2023 14:01
• 0 votes

1. Community
2. Documentation Questions
3. Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?

Hi David Benjamin, Thank you for answering my queries. Would it be possible to expand on the answer to Q3 above a little further: 1. How does trimming lead to having a Linked De Bruijn graph as you...

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• ISmolicz
• April 26, 2023 12:55
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

Hi David Benjamin, Thank you for your reply and for the advice that --linked-de-bruijn-graph should be the default now. Just to mention in case this is helpful, Mutect2 documentation advises that t...

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• ISmolicz
• April 25, 2023 22:22
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

Hi David Benjamin, Thank you for your reply to my post above. Please may I ask why using the --linked-de-bruijn-graph is not an argument that is set to true by default and is only recommended when ...

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• ISmolicz
• April 23, 2023 21:44
• 0 votes

1. Community
2. General Discussion
3. Expected variants not detected by Mutect2

Hi David Benjamin, Thank you for your reply to my post. By changing the arguments --genotype-germline-sites and --genotype-pon-sites to true, what does this change in the Mutect2 output? Would vari...

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• ISmolicz
• April 23, 2023 21:24
• 0 votes