GE
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Activity overview
Latest activity by GE-
GE commented,
Thank you
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GE commented,
Hi, This is the recommended best practices Mutect2 pipeline from Terra: https://app.terra.bio/#workspaces/help-gatk/Somatic-SNVs-Indels-GATK4/workflows/help-gatk/2-Mutect2-GATK4 https://dockstore.o...
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GE commented,
Sure. Note that if others think this is useful, a compromise might be to add to the tag "NOT-USED", so that the description of the tag is still present, but the user also can see that it was not ap...
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GE commented,
Thanks. That makes sense. The only part I think should be evaluated in future GATK versions is: "Regarding the VCF header, we do not change the header based on whether or not a certain filter was a...
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GE created a post,
FilterAlignmentArtifacts - only emitting PASS variants
AnsweredHi, FilterAlignmentArtifacts only emits PASS variants. Is this expected behavior? I would expect it would just add 'alignment' filter and output all variants. Otherwise it prevents users from fine-...
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GE created a post,
Missing documentation on strict_strand
AnsweredHi, The strict_strand filter in FilterMutectCalls is listed in the output VCF header regardless of whether it is actually applied, but it is only applied when the --min-reads-per-strand setting is ...
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GE created a post,
strand_bias filtering is never emitted
AnsweredHi, I am running Mutect2 4.1.9.0 using the latest Terra pipeline. Although in the VCF header, the strand_bias FILTER is listed, it is never applied to any variants across 5 different samples. At th...
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GE commented,
I made it with Picard BedToIntervalList, so it must be option A. I would recommend GATK add auto-detection of format for intervals. interval_list, list, intervals as extensions can be confusing.
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GE commented,
In a multi-sample analysis with 2 tumor samples vs 1 normal, if a somatic mutation is high quality in one of the tumor samples, but absent from the other tumor sample, will it be called? In other w...
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GE created a post,
1 year-old bug in libgkl that has not been fixed affecting FilterAlignmentArtifacts and HaplotypeCaller
Hi, See this bug on github: https://github.com/broadinstitute/gatk/issues/5690 It has been 1 year and still not fixed. It affects all tools that use smith waterman alignment from libgkl. Errors sti...