svdetect.sh Files

# svdetect.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 2.1.1
# Date: Jan 31, 2019


[Introduction]

svdetect.sh is a shell script to run SVDetect to detect SV in exome-seq and Shatterproof to detect chromothripsis. The output files of SVDetect are further annotated by gene.

[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. Install the following perl modules:
	
	$ perl -MCPAN -e shell
	> install Config::General
	> install Tie::IxHash
	> install Parallel::ForkManager
	> install Statistics::Distributions

3. The followingsfolders must be placed in the /path/to/programs.

	SVDetect_r0.8b
	hg19.len
	Shatterproof-0.1
        gene_loc
        svdetect_annovate.sh

   Prebuilt SVDetect_r0.8b and hg19.len can be downloaded at https://sourceforge.net/projects/svdetectcnv-sh.
   gene_loc files can be created by followings:
        
        download http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
        zcat refFlat.txt.gz | awk -F '\t' '{print $3"\t"$5"\t"$6"\t"$1}' | sort -t "`echo -e "\t"`" -k1,1 -k2,2n -u | awk -F '\t' '{print $2 "\t" $3 "\t" $4 >>"gene_loc_" $1}'
        copy the files to /path/to/programs/gene_loc

        The compressed gene_loc can be downloaded here.

4. You may need to install Shatterproof. 
	
	cd /path/to/programs/Shatterproof-0.14
	perl Makefile.PL
	sudo make
	make install

5. 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.

6. 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

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

	/path/to/outputfile/samplename/exome/samplename.SAM
        
        or

	/path/to/outputfile/samplename/exome/samplename.marked.realigned.fixed.recal.bam


8. Shatterproof uses the adjusted.bedgraph file produced by contra.sh. The file should be saved as following:
	
	/path/to/outputfile/samplename/exome/contra/samplename.adjusted.bedgraph.txt
       

[RUNNING]

Syntax:  sh svdetect.sh sample_name(requird) suffix(requird) 
	
	options:
        -bam: use bam (default)
        -sam: use sam
	-s: shutdown after finished
	-kt: keep temporary files


	ex:
	  sh svdetect.sh tumor fastq.gz  
     	  sh svdetect.sh tumor fastq -s