contra.sh Files

# contra.sh
# Author: Chin-Chen Pan
# Directore, General and Surgical Pathology
# Professor, attending pathologist
# Department of Pathology and Laboratory Medicine
# Taipei Veterans General Hospital
# TAIWAN
# Version 1.1.1
# Date: July 12, 2017


[Introduction]

contra.sh is a shell script to run contra-cnv mode. In addition to the original outputs of SVDetect, the script also outputs and bed.graph and an adjusted bed.graph with baseline adjusted to the average Log2Ratio of a certain chromosome or all chromosomes, and a sorted density file.

[Before running]

1. Prepare exome_test.config. The file contains four words in one line. No other words and lines are allowed.

	/path/to/programs /path/to/inputfile /path/to/outputfile thread_number

	ex1: 
	/home/user_name	/media/user_name/disk1/input /home/user_name/output 8

	ex2:
        ~  ~/input ~/output 8

2. The followings files and folders must be placed in the /path/to/programs.

	CONTRA.v2.0.8
	target.bed

3. Install python, R, bedtools and latest samtools

        sudo apt-get install python-dev
        sudo apt-get install r-base
        sudo apt-get install bedtools
        install samtools from samtools-1.5 to /path/to/samtools
        sudo cp /path/to/samtools/bin/samtools /usr/bin (compiled samtools is provided here)
    
4. The sam or bam file of sample and reference_mate should be named and put in the following folders compatible with exome_test.sh

	-bam (default)
        /path/to/outputfile/$1/exome/$1.marked.realigned.fixed.recal.bam
	/path/to/outputfile/$2/exome/$2.marked.realigned.fixed.recal.bam

        -sam
	/path/to/outputfile/$1/exome/$1.SAM
	/path/to/outputfile/$2/exome/$2.SAM
        if $1.BAM or $2.BAM is present, the BAM files will be used instead of SAM files.
        or

[RUNNING]

Syntax:  sh contra.sh sample_name(requird) reference_mate_name(requird) chrN(optional)
         Give the chrN if you want to adjust the baseline to the average Log2Ratio of that chromosome. If chrN is not given or given as "chr", the average Log2Ratio of all chromosomes will be used to adjust the baseline.
	
	options:
        -bam: use bam (default)
        -sam: use sam
	-s: shutdown after finished
	-kt: keep temporary files


	ex:
	  sh contra.sh tumor normal 
          sh contra.sh tumor chr8 -sam
 	  sh contra.sh tumor normal chr -s