Command: call

Call peaks in a .ccf file

Required parameters:

  • -i, –input INPUT: input .ccf file

  • output: output bed file

  • Either:

    • -p, –pValueCutoff PVALUECUTOFF: p-value cutoff (NOTE: This is a straight cutoff and will not take into account multiple hypothesis correction!), OR

    • -a, –alpha ALPHA: alpha for multiple hypothesis correction (must be between 0 and 1) AND

    • –correction CORRECTION: if alpha provided, need to specificity method of multiple hypothesis correction. See statsmodels.stats.multitest for a complete list of choices (default: bonferroni)

  • -bg, –background BACKGROUND: Background .ccf file

Optional parameters:

  • -r, –regions REGIONS: Regions over which to normalize event counts; should be supplied as a BED file. If not provided, the input file will be segmented using Bayesian blocks. (all options from blockify segment are available)

  • –intermediate INTERMEDIATE: Intermediate file to write verbose output (CSV format)

  • -d, –distance DISTANCE: Merge features closer than this distance (bp)

  • –min MIN: Report peaks larger than this cutoff (bp)

  • –max MAX: Report peaks smaller than this cutoff (bp)

  • -t, –tight: Shrink peak boundaries to overlap data points

  • -c, –pseudocount PSEUDOCOUNT: Pseudocount for background regions (default: 1)