yangjw
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Activity overview
Latest activity by yangjw-
yangjw commented,
Hi, David, thank you for your reply and advice! Well, I haven't figure out what exactly cause 16507G missing. Because the other variants are called correctly and none of them is missing. I guess ma...
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yangjw created a post,
GATK 4.3.0.0 Mutect2 fail to call variant
AnsweredREQUIRED for all errors and issues: a) GATK version used: 4.3.0.0b) Exact command used: --linked-de-bruijn-graph true --max-reads-per-alignment-start 0 c) Entire program log: run sucess. See detia...
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yangjw commented,
Hi, David, thank you for your reply. I set the '--downsampling-stride 50' and get the ideal result. Your advice helps me a lot! Thank you again!
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yangjw commented,
Hi Genevieve， I have met the same problem when I used GATK 4.3.0.0 Mutect2. Here is an example. I haven't use FilterMutectCalls, but I don't know how to deal with such variants. Some of them seems ...
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yangjw created a post,
Asking for advice on Mutect2 calling in somatic but amplicon data
Hi, GATK team! a) GATK version used: 4.3.0.0b) Exact command used: Mutect2 --mitochondria-modec) Entire program log: running sucess but confused by the results with differen parameters I am analys...