Version 0.0

Peak-calling for genomic enrichment assays of treatment sample(s) (-t [<file>]+), with or without control sample(s) (-c [<file>]+). Input files must be in SAM/BAM format. Incorporates ideas from SAMtoBED, removeChrom, and MACS2 v2.1.2_dev.

• Control of analysis of alignments:
  • Properly paired alignments only (default); fragments are inferred appropriately
  • Also keeping unpaired alignments:
    • As they appear in the SAM/BAM file (-y)
    • Length increased to specified value (-a <int>)
    • Length increased to average value of paired alignments (-x)
• Filtering options:
  • Chromosomes (reference sequences) to ignore (-e <arg>)
  • Minimum mapping quality (-m <int>)
• Peak-calling options:
  • Maximum q-value (-q <float>, def. 0.05)
  • Maximum p-value (-p <float>)
  • Minimum length of a peak (-l <int>, def. 100bp)
  • Maximum distance between significant sites (-g <int>, def. 100bp)
• Output options:
  • Output peak file, in ENCODE narrowPeak format (-o <file)
  • Output bedgraph file listing treatment/control pileups and p/q values (-b <file>)