1. Community
2. Somatic
3. Variant called in reads from ArtificialHaplotypeRG

Hi Genevieve Brandt (she/her), I am also observing reads in the Read group 'ArtificialHaplotypeRG' in the BAM that is generated when running Mutect2 with --bamout. I am using GATK 4.2.0.0. Followin...

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• ISmolicz
• June 17, 2021 11:46
• 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?

Thank you for your reply Genevieve Brandt (she/her). I completely understand it is taking time to answer my other query so will await an update once information is available. Although MergeBamAlign...

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• ISmolicz
• April 29, 2021 19:33
• 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?

Thank you for your reply Genevieve Brandt (she/her). I think it would be useful to clarify in the documentation that the adapters would not be removed when processing data through BWA-MEM when appl...

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• ISmolicz
• April 29, 2021 11:30
• Edited
• 0 votes

1. Community
2. General Discussion
3. Adapter trimming: how can permanent adapter trimming, or hard clipping, be achieved when following GATK Best Practices and commencing data preprocessing with uBAM files?

Thank you for the additional information SkyWarrior. I have previously questioned why permanent hard clipping is not a supported option within GATK workflows as there are many external recommendati...

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• ISmolicz
• April 08, 2021 13:37
• Edited
• 0 votes

1. Community
2. Documentation Questions
3. BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used?

Thank you for your reply Genevieve Brandt. At present, I am using an interval list with the following GATK tools: GenomicsDBImport, Mutect2, GetPileupSummaries and DepthOfCoverage. In addition, I u...

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• ISmolicz
• April 07, 2021 17:32
• 0 votes

1. Community
2. General Discussion
3. Adapter trimming: how can permanent adapter trimming, or hard clipping, be achieved when following GATK Best Practices and commencing data preprocessing with uBAM files?

Thank you for your reply and advice SkyWarrior. I have read information in multiple resources and legacy forum posts and understand there is not a straightforward answer. Could I ask what it was in...

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• ISmolicz
• April 07, 2021 15:10
• 0 votes

1. Community
2. General Discussion
3. How do I input two separate paired-end fastq files into the GATK pipeline? Do I use an interleave-fastq?

Hi Lauren Fedenia, What tool are you planning to use with the FASTQ file(s)? Kind regards.

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• ISmolicz
• April 06, 2021 16:55
• 0 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. 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. Other
3. Error when trying to generate the second recalibration table for AnalyzeCovariates

Hi Genevieve Brandt, Thank you for letting me know and for setting up this ticket. I will ensure I check the relevant page for updates. Kind regards.

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• ISmolicz
• March 02, 2021 17:55
• 0 votes