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
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
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
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.