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