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scan

scan the reference genome to get microsatellites information

   Usage:  msisensor-pro scan [options]

   -d   <string>   reference genome sequences file, *.fasta or *.fa format  [required]
   -o   <string>   output homopolymers and microsatellites file [required] 

   -l   <int>      minimal homopolymer(repeat unit length = 1) size, [default=8]
   -c   <int>      context length (5-32), [default=5]
   -m   <int>      maximal homopolymer size, [default=50]
   -s   <int>      maximal length of microsatellite (1-32) , [default=6]
   -r   <int>      minimal repeat times of microsatellite(repeat unit length>=2), [default=5]
   -p   <int>      output homopolymer only, 0: no; 1: yes, [default=0]
   -h   help

msi

evaluate MSI using paired tumor-normal sequencing data (msisensor)

   Usage:  msisensor-pro msi [options]

   -d   <string>   homopolymers and microsatellites file [required]
   -n   <string>   normal bam file with index [required]
   -t   <string>   tumor  bam file with index [required]
   -g   <string>   reference file [required if *.cram for -t]
   -o   <string>   output path (Ending with a slash is not allowed.) [required] 

   -f   <double>   FDR threshold for somatic sites detection, [default=0.05]
   -c   <int>      coverage threshold for msi analysis, WXS: 20; WGS: 15, [default=15]
   -z   <int>      coverage normalization for paired tumor and normal data, 0: no; 1: yes, [default=0]
   -p   <int>      minimal homopolymer size for distribution analysis, [default=8]
   -m   <int>      maximal homopolymer size for distribution analysis, [default=50]
   -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=1]
   -h   help

pro

evaluate MSI using single (tumor) sample sequencing data

   Usage:  msisensor-pro pro [options]

   -d   <string>   homopolymers and microsatellites file [required] 
   -t   <string>   bam/cram file of tumor/normal(for baseline building) sample [required] 
   -g   <string>   reference file [required if *.cram for -t]
   -o   <string>   output path (Ending with a slash is not allowed.) [required]

   -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=15]
   -p   <int>      minimal homopolymer size for distribution analysis, [default=8]
   -m   <int>      maximal homopolymer size for distribution analysis, [default=50]
   -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 microsatellite only, 0: no; 1: yes, [default=0[
   -0   <int>      output site have no read coverage, 1: no; 0: yes, [default=1]
   -h   help

baseline

build baseline for tumor only detection

   Usage:  msisensor-pro baseline [options]

   -d   <string>   homopolymer and microsatellite file [required]
   -i   <string>   configure files for building baseline (text file) [required]
        you need to provide the output (*_all) from pro command 
        e.g.
         ----------------------------------
          case1	/path/to/case1_sorted_all 
          case2	/path/to/case2_sorted_all 
          case3	/path/to/case3-sorted_all 
         ----------------------------------
   -o   <string>   output path for baseline [required] 

   -s   <double>   microsatellite sites with support from fewer than -d samples will not pass quality control, [default=10]
   -h   help