bam_vs_bam.py - compute coverage correlation between bam files

Tags

Genomics NGS BAM Comparison

Purpose

Compare per base coverage between two bam formatted files.

Usage

Example:

python bam_vs_bam.py in1.bam in2.bam

This command generates a tab delimited output with columns chromosome, base coordinate, number of overlapping reads in in1.bam, and number of overlapping reads in in2.bam.

Type:

python bam_vs_bam.py --help

for command line help.

Documentation

This tools allows users to compare the per base coverage between two BAM files. The output includes all bases in the supplied reference fasta except those with no coverage in the input BAMs.

At present the –interval or -i option has not been implemented.

Command line options

--regex-identifier

supply a regex to extract an identifier from the filenames. defualts to using the filename

usage: bam-vs-bam [-h] [--version] [-i FILENAME_INTERVALS]
                  [-e REGEX_IDENTIFIER] [--timeit TIMEIT_FILE]
                  [--timeit-name TIMEIT_NAME] [--timeit-header]
                  [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                  [--log-config-filename LOG_CONFIG_FILENAME]
                  [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                  [-E STDERR] [-S STDOUT]
bam-vs-bam: error: argument -?: expected one argument