ISmolicz
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Activity overview
Latest activity by ISmolicz-
ISmolicz commented,
Dear Genevieve Brandt (she/her), Nabeel Ahmed and the GATK Team, Please could you advise if the issue described in the original post and comments was resolved? If so, please could you advise on the...
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ISmolicz created a post,
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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ISmolicz commented,
Dear David Benjamin and the GATK Team, Reading the post above written by Nicolas Loucheu, multiple steps were taken to try and resolve the issue described. This included steps mentioned in the foll...
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ISmolicz commented,
Dear Nicolas Loucheu, Please may I ask if you managed to resolve the issue described in your initial post above? If so, what was the cause, and please could you advise on how it was resolved? Thank...
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ISmolicz created a post,
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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ISmolicz commented,
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 commented,
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 commented,
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 commented,
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 commented,
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...