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