JUNHUI LI
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Activity overview
Latest activity by JUNHUI LI-
JUNHUI LI commented,
Thanks for the clarification, Gökalp Çelik . Is there a feature in GATK that can perform this normalization? Thanks,Junhui
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JUNHUI LI created a post,
how to set parameters value in DepthOfCoverage matched the default value in mutect2
Hi there, I am planning to normalize the somatic mutation rate across samples using DepthOfCoverage. To maintain consistency with Mutect2, which uses --min-base-quality-score of 10 and --base-quali...
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JUNHUI LI commented,
Hi Gökalp Çelik, Thanks. Here are two variants called with version 4.6.0.0 chr1 42256836 . C T . . AS_SB_TABLE=20,21|2,2;DP=45;ECNT=4;ECNTH=2;MBQ=20,20;MFRL=...
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JUNHUI LI commented,
Thanks, Gökalp Çelik. This issue is still there in GATK version 4.6.0.0. I would appreciate any recommendations you might have for working around this issue. --Junhui
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JUNHUI LI created a post,
GATK Mutect2 counts the alternate base twice in overlapping paired reads
REQUIRED for all errors and issues: a) GATK version used: 4.1.8.1Hi GATK team, I observed a significant increase in variant calls in samples with overlapping paired reads and discovered that Mutect...
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JUNHUI LI created a post,
ASEReadCounter output wrong number of coverage
Hi, I am using ASEReadCounter to count the number of reads per variant in a BAM file. For some positions, it will report 1 read covered(1 refCount or 1 altCount) while there is no read covered at t...