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vardict can not call the mutation correctly #383

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wyy1234-github opened this issue Mar 23, 2023 · 0 comments
Open

vardict can not call the mutation correctly #383

wyy1234-github opened this issue Mar 23, 2023 · 0 comments

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@wyy1234-github
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wyy1234-github commented Mar 23, 2023

hi,
I am using vardict to call snv/indel, but i find it can not call the mutation correctly,the following is the igv sight, G>C is the main mutation
image
I use the code as follow:
java -jar VarDict-1.8.3.jar -G hg19.fa
-f 0.002 -N 2022WSSW004697-T -b 2022WSSW004697-T.rmdup.bam
-r 3 -th 20 -c 1 -S 2 -E 3 -g 4 -R chr11:69457890 | teststrandbias.R
| var2vcf_valid.pl -N 2022WSSW004697-T -E -f 0.002

and I just get the G>T mutation.
image

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