TA
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Activity overview
Latest activity by TA-
TA created a post,
Mutect2 low allele fraction mutation calling
Hi, I have two questions on low fraction mutations: Question 1: I wanted to know if Mutect2 had been validated on calling extremely low fraction VAF mutations (as can be found in ctDNA). Are there ...
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TA commented,
Hi Genevieve, Ok got it. Currently it is not throwing an error. It seems to resolve the conflict by using the @RG tag information from the unaligned BAM. This created an issue for me later on as du...
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TA created a post,
MergeBamAlignment conflicting headers between mapped and unmapped
AnsweredHi, I wanted to ask how MergeBamAlignment deals with conflicting header information. Specifically if the unmapped BAM and mapped BAM have different @RG tags in the header then how does it resolve? ...
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TA commented,
Got it thank you for your quick response!
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TA commented,
Hi, To follow-up on this question: does PON blacklist sites or specific variants? For example, if the PON has a A>C SNV, but the tumor has ALT reads supporting A>T, is this site labeled as PON and...
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TA commented,
Hi, I used gatk 4.2.0.0 We ran on terra referencing broad gatk docker us.gcr.io/broad-gatk/gatk@sha256:f2602e0bbc0117c30d23d8d626eb8d0a21ca672bb71180b5cf25425603a0ae09
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TA created a post,
Mutect2 genotype-germline-sites filtering discrepancy
AnsweredHi, I have a few technical questions about changes in filtered variants when running mutect2 with -genotype-germline-sites. I ran mutect2 on matched tumor-normal data with and without -genotype-ger...