somatic.sh Files

# somatic.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 2.2.1
# Date: Feb. 8, 2021

[Introduction]

somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV.

[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. pyhton and jre must be installed.

	sudo apt-get install python-dev
	sudo apt-get install openjdk-8-jdk

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

	VarScan.v2.3.9.jar
	annovar
	vs_format_converter.py
	clinvar
	cosmic
	dbSNPnew
   
    For annovar, download the followings filters.
	perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
	perl annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/
	perl annotate_variation.pl -buildver hg19 -downdb genomicSuperDups humandb/ 
	perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar esp6500siv2_all humandb/
	perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2014oct humandb/
	perl annotate_variation.pl -buildver hg19 -downdb phastConsElements46way humandb/
	perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar clinvar_20150330 humandb/
        perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp30a humandb/
        perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03nontcga humandb/


	Download left-normalized avsnp (hg19_avsnp150.txt) from ANNOVAR site.
     
        Use the script dbsnpnew.sh cosmicnew.sh and clinvarnew.sh to make dbSNP cosmic and clinvar files. 

	These files are tab-delimited. The format should look like this:

		rs990360547	chr10-100000035C-T
		rs946241909	chr10-100000101T-C
		rs923734382	chr10-100000126A-G
		rs894795669	chr10-100000179C-T
	  	
    Download vs_format_converter.py from https://github.com/PoisonAlien/varscan_accessories/blob/master/vs_format_converter.py
    
4. The splitted mpileup files Sample.chr[1-22,XY].mpileup and Normal.chr[1-22,XY}.mpileup must be saved in /path/to/outputfile/Sample/exome/mpileup

[RUNNING]

Syntax:  sh somatic.sh Sample Normal -options
	
	options:
	 -s: shutdown after finished

	ex:
	  sh somatic.sh BrCA1T Normal -s