NAME¶

bam-read - Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.

SYNOPSIS¶

Currently captured:

- name
- bases mapped
- edit distance
- bridges
- length
- reads mapped
- both mapped
- proper pair
- good
- uncovered bases
- mean mapq
- probability of coverage not being segmented

DESCRIPTION¶

bam-read version 1.0.0 Usage: bam-read <bam_file> <output_csv> <nullprior (optional)>

example: bam-read in.bam out.csv 0.95

Usage: bam-read <bam_file> <output_csv> <nullprior (optional)>

example: bam-read in.bam out.csv 0.95