Key Commands

Usage:

   msisensor-pro <command> [options] 

Commands:

scan (from msisensor)

options:

    -d   <string>   reference genome sequences file, *.fasta format 
    -o   <string>   output homopolymers and microsatellites file 

    -l   <int>      minimal homopolymer size, default=5 
    -c   <int>      context length, default=5 
    -m   <int>      maximal homopolymer size, default=50 
    -s   <int>      maximal length of microsate, default=5 
    -r   <int>      minimal repeat times of microsate, default=3 
    -p   <int>      output homopolymer only, 0: no; 1: yes, default=0 
   
    -h   help 

baseline

options:

   -d   <string>   homopolymer and microsatellite file
   -i   <string>   configure files for building baseline (text file) 
        e.g.
          case1	/path/to/case1_sorted.bam
          case2	/path/to/case1_sorted.bam
          case2	/path/to/case1-sorted.bam
   -o   <string>   output directory

   -c   <int>      coverage threshold for msi analysis, WXS: 20; WGS: 15, default=20
   -0   <int>      output site have no read coverage, 1: no; 0: yes, default=0
   
   -h   help

msi (from msisensor)

options:

   -d   <string>   homopolymers and microsatellites file
   -n   <string>   normal bam file
   -t   <string>   tumor  bam file
   -o   <string>   output prefix

   -e   <string>   bed file, optional
   -f   <double>   FDR threshold for somatic sites detection, default=0.05
   -c   <int>      coverage threshold for msi analysis, WXS: 20; WGS: 15, default=20
   -z   <int>      coverage normalization for paired tumor and normal data, 0: no; 1: yes, default=0
   -r   <string>   choose one region, format: 1:10000000-20000000
   -l   <int>      minimal homopolymer size, default=5
   -p   <int>      minimal homopolymer size for distribution analysis, default=10
   -m   <int>      maximal homopolymer size for distribution analysis, default=50
   -q   <int>      minimal microsatellite size, default=3
   -s   <int>      minimal microsatellite size for distribution analysis, default=5
   -w   <int>      maximal microsatellite size for distribution analysis, default=40
   -u   <int>      span size around window for extracting reads, default=500
   -b   <int>      threads number for parallel computing, default=1
   -x   <int>      output homopolymer only, 0: no; 1: yes, default=0
   -y   <int>      output microsatellites only, 0: no; 1: yes, default=0
   -0   <int>      output site have no read coverage, 1: no; 0: yes, default=0
   
   -h   help

pro

 options:

   -d   <string>   homopolymer and microsates file
   -t   <string>   tumor bam file
   -o   <string>   output prefix

   -e   <string>   bed file, optional
   -i   <double>   minimal threshold for instable sites detection (just for tumor only data), default=0.1
   -c   <int>      coverage threshold for msi analysis, WXS: 20; WGS: 15, default=20
   -r   <string>   choose one region, format: 1:10000000-20000000
   -p   <int>      minimal homopolymer size for distribution analysis, default=10
   -m   <int>      maximal homopolymer size for distribution analysis, default=20
   -s   <int>      minimal microsatellite size for distribution analysis, default=5
   -w   <int>      maximal microsatellite size for distribution analysis, default=20
   -u   <int>      span size around window for extracting reads, default=500
   -b   <int>      threads number for parallel computing, default=1
   -x   <int>      output homopolymer only, 0: no; 1: yes, default=0
   -y   <int>      output microsatellite only, 0: no; 1: yes, default=0
   -0   <int>      output site have no read coverage, 1: no; 0: yes, default=0
   
   -h   help