meerkat.sh Files

# meerkat.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: Aug 18, 2017

[Introduction]

meerkat.sh is a shell script to run Meerkat for SV detection in Exome-seq. The script accepts single BAM or paired tumor-normal BAMs.

[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. Meerkat uses old version of samtools (samtools-0.1.19). Download prebuilt samtools here, decomress and copy the folder to the /path/to/programs.

3. Install BWA and Blast2. Blast2 has been deprecated by NCBI. You may download it from the NCBI legacy site or simply install it from Ubuntu app center or using apt-get. 
        
        sudo apt-get install bwa
        sudo apt-get install blast2

4. You may need to download BioPerl. If you're asked to install Bio::DB::Fasta, download the BioPerl package.

        #perl -MCPAN -e shell
        >install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

5. Decompress chromFa.tar.gz into /path/to/programs/chromFa, Keep chr1.fa to chr22.fa, chrM.fa, chrX.fa, chrY.fa. Delete others. The program will automatically build the index and create directory.index. The directory.index can be downloaded here.

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

	Meerkat
        samtools-0.1.19/samtools
        chromFa
        rmsk-hg19.txt
        refGene_sorted.txt
 
7. The script uses the BAM produced by exome_test.sh. e.g.

	/path/to/outputfile/T_name/exome/T_name.marked.realigned.fixed.recal.bam
        /path/to/outputfile/T_name/exome/T_name.marked.realigned.fixed.recal.bai
	/path/to/outputfile/N_name/exome/N_name.marked.realigned.fixed.recal.bam
        /path/to/outputfile/N_name/exome/N_name.marked.realigned.fixed.recal.bai


[RUNNING]

Syntax:  sh meerkat.sh T_name(required) N_name(optional) -options
	
	options:
         -kt: keep temporary files
	 -s: shutdown after finished

	ex:
	  sh meerkat.sh BrCA1 
          sh meerkat.sh T1 N1 -kt -s

Note: The script is designed to start from the last process. However, please delete the incomplete temporary files after the last completed file.