G E
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Activity overview
Latest activity by G E-
G E created a post,
MergeMutectStats missing from documentation
Hi, MergeMutectStats is missing from your online documentation of GATK.
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G E commented,
I just tested GATK 4.4 - it gives the same error. Reducing max gaussian is not a fix, because per Specs of this tool it should work on 3 whole genomes. So this is a bug. Can you advise on next step...
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G E created a post,
Bug in VariantRecalibrator: Data not found
GATK v4.1.4.0 VariantRecalibrator step I got the below error that several people have reported before. None of the reasons prior users have received this apply to my situation. This was run on 3 wh...
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G E created a post,
Novaseq X - OPTICAL_DUPLICATE_PIXEL_DISTANCE
Hello, What OPTICAL_DUPLICATE_PIXEL_DISTANCE should be used in Picard Markduplicates for the new Novaseq X 10B flow cells?
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G E commented,
Hello, Just following up on the above question that hasn't been answered yet. Is there an option for MarkDuplicates to only remove or tag optical duplicates, but not PCR duplicates?
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G E commented,
1) Does turning on --genotype-germline-sites or --genotype-pon-sites change anything about the downstream filtering process (e.g. FilterMutectCalls and FilterAlignmentArtifacts)? I just want to mak...
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G E commented,
Is there any way to set a threshold VAF for germline and PON sites in the normal sample below which they are genotyped by Mutect2? This is an important issue, because true low-level mosaic variants...
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G E commented,
Thank you! Regarding Question 2- What are the criteria used for filtering germline sites before running the assembly graph? The algorithm for that are not clear from the Mutect2 PDF documentation.
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G E commented,
Hi Bhanu, Thanks for the follow-up. However, while I appreciate the Bayesian argument here, and the fact that it is more likely to be a "false negative dropout" in the mother than a de novo variant...
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G E commented,
Not completely for question (2). There seem to be two steps where Mutect2 can filter germline variants. Once when Mutect2 is running where those variants never show up at all in the final VCF, and ...