Will create mpileup files from both tumor and normal using 2-cores, create necessary files that are needed for Sequenza and run R script that will run Sequenza on a command line interphase.
sh sequenza_fromBam.sh <normal.bam> <tumor.bam> <sampleName> <reference.fasta>This command will generate all sequenza input files, and output files in the current working directory with prefix as .
If an mpileup file already exists, there is no need to re-generate bamfile. One can use the following command instead.
sh sequenza_fromMpileup.sh <normal.pileup> <tumor.pileup> <sampleName>If you already have a seqz file to be used for Sequenza you can use the following script
Rscript run_sequenza.R --seqz_file <seqzFile> --output_dir <output_dir> --sample_name <sampleName>