lethalfang/scalpel repository overview

⁠Example command

docker run -v /:/mnt -i lethalfang/scalpel:0.5.3
/opt/scalpel-0.5.3/scalpel-discovery --somatic
--ref /mnt/ABSOLUTE/PATH/TO/GRCh38.fa
--bed /mnt/ABSOLUTE/PATH/TO/Sequencing_Capture.bed
--normal /mnt/ABSOLUTE/PATH/TO/Matched_Normal.bam
--tumor /mnt/ABSOLUTE/PATH/TO/Tumor.bam
--window 600
--dir /mnt/ABSOLUTE/PATH/TO/RESULTS/scalpel

docker run -v /:/mnt -i lethalfang/scalpel:0.5.3 bash -c
"/opt/scalpel-0.5.3/scalpel-export --somatic
--db /mnt/ABSOLUTE/PATH/TO/RESULTS/scalpel/main/somatic.db.dir
--ref /mnt/ABSOLUTE/PATH/TO/GRCh38.fa
--bed /mnt/ABSOLUTE/PATH/TO/Sequencing_Capture.bed
> /mnt/ABSOLUTE/PATH/TO/RESULTS/scalpel/scalpel.vcf"

cat /ABSOLUTE/PATH/TO/RESULTS/scalpel/scalpel.vcf |
docker run -v /:/mnt -i lethalfang/scalpel:0.5.3 /opt/vcfsorter.pl /mnt/ABSOLUTE/PATH/TO/GRCh38.dict -
> /ABSOLUTE/PATH/TO/RESULTS/Scalpel.vcf