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bam-read - Parse bam files after multi-mapping reads have been assigned and

BAM-READ(1) User Commands BAM-READ(1)

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
September 2015 bam-read version 1.0.0