allmut Files

# allmut.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 3.3.1
# Date: Sep 4, 2019

[Introduction]

allmut.sh is a shell script to run MutSigCV and genvisr.

[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 MCR901. Download MCR_R2016a_glnxa64_installer.zip and install the MCR901 to /path/to/programs/MCR901/v901.

3. Install MutSigCV_1.41 to /path/to/programs.

4. Install genvisr
        sudo R (>3.5)
        if (!requireNamespace("BiocManager", quietly = TRUE))
          install.packages("BiocManager")
        BiocManager::install("GenVisR")

5. Unzip chr_files_hg19.zip (download from https://software.broadinstitute.org/cancer/cga/mutsig_run) to /path/to/programs. 

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

	chr_files_hg19 or chr_files_hg38
        MCR901/v901
        MutSigCV_1.41
        gene.covariates.txt
        mutation_type_dictionary_file.txt
	genvisr.tmp

    Some files can be downloaded here.

7. genvisr.tmp is used as the template to run genvisr.
    
8. Put the maf files to be catenated into one file in the folder of /path/to/inputfile/prefix (e.g. br1.maf br2.maf,...).

9. A script tcga2maf.sh is provided to transform TCGA MAF file to MAF file compatible with this script.

[RUNNING]

Syntax:  sh allmut.sh prefix_of_inputfile prefix_of_outputfile
         options: 
             -hg19: Use hg19 (default)
             -hg38: Use hg38
             -md: provide additional files using most deleterous mutations 
                  ("Missense_Mutation", "Nonsense_Mutation", "Frame_Shift_Ins", "Frame_Shift_Del", "In_Frame_Ins", "In_Frame_Del")
             -s: shutdown after finished
	
	ex:
	  sh allmut.sh breastca/br breastca -hg38



[Appendix]
If you want to run MutSigCV on hg38, please do followings:

1. Download hg38.chromFa.tar.gz (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz) and unzip to hg38 folder.
2. Go to hg38 folder, ls the files to filelist (provided here).
3. Run the following script.

mkdir -p /path/to/programs/chr_files_hg38
while read -r line
do
 name="$line"
 echo "Doing $name"
 cat $name | grep -v ">"|awk '{printf $1 > "/path/to/programs/chr_files_hg38/"substr("'"$name"'", 1, index("'"$name"'",".")) "txt" }'
done < filelist