SGSeq is an R package. Therefore our ENTRYPOINT.sh script for SGSeq calls an R script to run the tool. The parameters listed here are the parameters given to the R script.
These are the default parameters set in the src/sgseq/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the SGSeq manual.
The path to the gene annotation file in GTF format for annotation of fusion junctions.--gtf $gtf
Name of bamfile.--path_to_bam $controlfolder/*filename*.bam
Output directory. The output will be separated into case and control folder based on the basefolder of the according bam file. If you are running the DICAST pipeline to compare different mapping tools this will include the name of the mapping tool of the used bam file.--out $outdir
Number of threads to be used during the computation--cores $ncores