/cmdcoverage

Be able to take a BAM file and output a quick command line graph of coverage

Primary LanguageShellApache License 2.0Apache-2.0

CMDcoverage

Version 0.2.1

Author: Greg Fedewa

Copyright: 2017.12.11

The whole idea here is to take a BAM file and be able to output a quick command line graph of coverage.

Usage:

cmdcoverage.sh [-h] [-a] <file.bam|file.sam> [windowsize]

OR

samtools mpileup [options] [region] <file.bam|file.sam> | cmdcoverage.sh [-a] [windowsize]

Requirements:

spark: for the single line graph (default)

gnuplot: for the multiline graph (-a)"