G E
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Activity overview
Latest activity by G E-
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 ...
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G E commented,
Awesome, that's reassuring.
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G E commented,
Thanks. Regardless of the meaning of the IUPAC codes, however, I was wondering why 1000 genomes uses these bases in the genome reference. This is not a standard reference usage (standard hg38 refer...
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G E commented,
Thanks for all your efforts. 1. Yes 2. Ped file: Family1 Sample1 0 0 1 1Family1 Sample2 0 0 2 1Family1 Sample3 Sample1 Sample2 1 2
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G E commented,
Thank you. Just to clarify regarding this: "Yes, Mutect2 can handle multi-allelic sites in the PON." -> Can Mutect2 handle multi-allelic sites that contain both indel and SNPs? i.e. mixed SNP + in...