---
name: "bam-read"
section: "1"
platform: "linux"
package: "transrate-tools"
version: "1.0.0-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bam-read"
---

# bam-read(1)

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

## 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