lethalfang/vardictjava repository overview

⁠Example command

docker run -v /:/mnt -i lethalfang/vardictjava:1.5.1
/opt/VarDict-1.5.1/bin/VarDict
-G /mnt/ABSOLUTE/PATH/TO/GRCh38.fa
-f 0.05 -h
-b '/mnt/ABSOLUTE/PATH/TO/Tumor.bam|/mnt/ABSOLUTE/PATH/TO/Matched_Normal.bam'
-Q 1 -c 1 -S 2 -E 3 -g 4 /mnt/ABSOLUTE/PATH/TO/Sequencing_Capture.bed
> /ABSOLUTE/PATH/TO/RESULTS/2017-08-02_15-24-38_179780621.var \

docker run -v /:/mnt -i lethalfang/vardictjava:1.5.1
bash -c "cat /mnt/ABSOLUTE/PATH/TO/RESULTS/2017-08-02_15-24-38_179780621.var | awk 'NR!=1' | /opt/VarDict/testsomatic.R | /opt/VarDict/var2vcf_paired.pl -N 'TUMOR|NORMAL' -f 0.05"
> /ABSOLUTE/PATH/TO/RESULTS/VarDict.vcf