svdetectcnv.sh Files

# svdetectcnv.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 4.1.1
# Date: Oct. 5, 2019


[Introduction]

svdetectcnv.sh is a shell script to run SVDetect CNV mode. In addition to the original outputs of SVDetect, the script also outputs 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.

	SVDetect_r0.8b
	hg19.len

3. The Exomeseq files must be paired end, and named as samplename_1.suffix and samplename_2.suffix. The suffix must be one of the fastq/fq/fastq.gz/fq.gz.

4. In order to be compatible for SOAPfuse, the Exomeseq files must be placed in the following paths:

	/path/to/inputfile/samplename/Lib/samplename_1.suffix
	/path/to/inputfile/samplename/Lib/samplename_2.suffix

5. The sam or bam file of sample and reference_mate should be named and put in the following folders compatible with exome_test.sh

	/path/to/outputfile/$1/exome/$1.SAM
	/path/to/outputfile/$2/exome/$2.SAM
        
        or

	/path/to/outputfile/$1/exome/$1.marked.realigned.fixed.recal.bam
	/path/to/outputfile/$2/exome/$2.marked.realigned.fixed.recal.bam
       

[RUNNING]

Syntax:  sh svdetectcnv.sh sample_name(requird) suffix(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
	-db: delete splitted bam


	ex:
	  sh svdetectcnv.sh tumor fastq.gz normal 
          sh svdetectcnv.sh tumor fastq normal chr8 -sam
 	  sh svdetectcnv.sh tumor fastq normal chr -s