seqz.sh Files

# seqz.sh 
# Author: Chin-Chen Pan 
# Directore, General and Surgical Pathology 
# Professor, attending pathologist 
# Department of Pathology and Laboratory Medicine 
# Taipei Veterans General Hospital 
# Version 3.2.1
# Date: Jan 11, 2021

[Introduction] seqz.sh is a shell script to run sequenza for exome-seq. The shell uses the files produced by exome_test.sh. 

[Before running] 
1. Install sequenza. git clone https://bitbucket.org/sequenza_tools/sequenza-utils cd sequenza-utils sudo python setup.py install 
2. Install R program. 
   sudo R source("https://bioconductor.org/biocLite.R") 
   biocLite("copynumber") 
   install.packages("sequenza") 
3. Copy seqz.tmp to /path/to/programs. Do not change the content of the file. It is used as a template for Rscript. 
4. Create hg19.gc50Base.txt.gz to /path/to/programs. 
   sequenza-utils.py GC-windows -w 50 /path/to/programs/hg19/hg19.fa | gzip > /path/to/programs/hg19.gc50Base.txt.gz 
5. The shell script will invoke R. Call it with sudo command. 
6. Download cnv_annotate.sh. Copy it to /path/to/programs. 
7. cytoband_loc files can be created by followings: 
   http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz 
   zcat cytoBand.txt.gz | cut -f1,2,3,4 | sort -t "`echo -e "\t"`" -k1,1 -k2,2n -u | awk -F '\t' '{print $2 "\t" $3 "\t" $4 >>"cytoband_loc_" $1}' 
   copy the files to /path/to/programs/cytoband_loc 

[RUNNING] 
Syntax: sudo sh seqz.sh sample_name mate_name output_directory -options 
options: 
  chrN: The chromosome number whose average Log2Ratio the baseline is adjusted to 
  -kt: keep temporary files 
  -s: shut down after finished 
  ex: sudo sh cnvkit.sh test normal cnv_output 3 -kt -s 
  echo 'password' | sudo -S sh seqz.sh test normal seqz_output chr3