ISmolicz
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What argument(s) should be used instead of --debug-graph-transformations?
Hello GATK Team, The documentation entitled 'When HaplotypeCaller and Mutect2 do not call an expected variant' suggests running Mutect2 with the argument --debug-graph-transformations set as true a...
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Why are full regions removed in the bamout file of Mutect2 when compared to the input files?
Dear GATK Team, As referred to in a separate post, in the (Notebook) Intro to using Mutect2 for somatic data documentation, there are two IGV images in the section 'REVIEW CALLS WITH IGV', and the ...
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Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?
Dear GATK Team, In the (Notebook) Intro to using Mutect2 for somatic data documentation, there are two IGV images in the section 'REVIEW CALLS WITH IGV', and the TP53 locus at chr17:7,666,402-7,689...
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How do I ensure sequence context-dependent artifacts, such as for FFPE deamination, are filtered using the current version of GATK?
Dear GATK Team, In previous (How to) Call somatic mutations using GATK4 Mutect2 guidance, it was possible to run the tool FilterByOrientationBias (EXPERIMENTAL) and an 'orientation bias' filter was...
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If base quality scores set at 2 for clipped regions are restored to the original score with MergeBamAlignment, how will clipped regions not contribute to downstream analyses?
PlannedDear GATK Team, In the tutorial (How to) Map and clean up short read sequence data efficiently, it states that MergeBamAlignment (Picard) 'restores original base quality scores'. My understanding i...
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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?
AnsweredDear GATK Team, In the tutorial (How to) Map and clean up short read sequence data efficiently, the documentation states that changing the base quality scores to 2 for a clipped region 'effectively...
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Adapter trimming: how can permanent adapter trimming, or hard clipping, be achieved when following GATK Best Practices and commencing data preprocessing with uBAM files?
Dear GATK Community, I understand there has already been a post regarding adapter trimming previously (Do I need to perform fastqc and adapters trimming before gatk pipeline?). However, many tools ...
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BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used?
AnsweredDear GATK Team, I have converted multiple BED files for a custom panel to Picard-style interval lists with BedToIntervalList (Picard) prior to merging them to form one interval list with IntervalLi...
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Error when trying to generate the second recalibration table for AnalyzeCovariates
Dear GATK Team, In previous GATK4 versions, I understand there was a -bqsr option to use with BaseRecalibrator so that a second recalibration table could be generated and then submitted to AnalyzeC...
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CreateSomaticPanelOfNormals: can a panel of normals be created from more than one GenomicsDB workspace?
Dear GATK Team, In the GATK 4.1.9.0 documentation, I see that the following is the example command for running CreateSomaticPanelOfNormals and one GenomicsDB workspace is specified: gatk CreateSom...