cnvHMM
cnvhmm (copy number analysis using Hidden Markov algorithm)
Version: 1.0.1
Author: Ken Chen & Xiaoqi Shi
Usage: cnvhmm <command> [options]
Key commands:
cnsdepth create depth file
hmm run HMM analysis
Usage: cnvhmm cnsdepth [options] cnsfile outputfile
Optional Arguments:
-y STRING assign marker file[default=NULL]
-q INT map quality cutoff[default=40]
-w INT window size[default=1000]
-b INT mininum position[default=1]
-e DOUBLE maximus position[default=1000000000000]
-m INT GC window size[default=1000]
-c FLOAT GC cutoff[default=0.5]
Usage: cnvhmm hmm [options] [cnsfile] [infile]
Optional Arguments:
-i if present program will use file created from cnsdepth as input[infile], otherwise take marker[markerfile] and cns[cnsfile] file as inputs
Parameters for depth & GC data preparation:
-y STRING assign marker file[default=NULL]
-d STRING create and write out depth file from marker and cns file
-o STRING results file(states and region information)
-q INT map quality cutoff[default=40]
-w INT window size[default=1000]
-b INT mininum position[default=1]
-e DOUBLE maximus position[default=999999999]
-m INT GC window size[default=1000]
-c FLOAT GC cutoff[default=0.5]
Parameters for HMM process:
-a STRING HMM algorithm [default='viterbi']
-n INT max copy number[default=3]
-f INT median filter size[default=3]
-g INT GC correction 1:apply 0:not apply[default=1]
-t INT transition probability 1:update 0:not update[default=0]
-r DOUBLE cnv rate[default=0.001]
-s DOUBLE nv size[default=0.1]
-k INT minimum number of markers[default=5]
-x INT The maximum # of bases a cnv can extend without evidence[default=450000]
-l DOUBLE Log Likelihood Ratio Cut off[default=10]
