BamTyper 0.2.6

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# Overview

Ability to work out the orientation and insert size of a paired read data file
Can estimate relative orientation and gap between pairs of contigs in the bam file (Useful for scaffolding)

# Installation

use pip:

```sh
$\text{You can't use 'macro parameter character \#' in math mode}$ bamtyper type bamfile.bam

Determining OT for BAM 'bamfile'
Orientation: IN Insert: 301, Stdev: 29

bamtyper links - Parse BAM files and get linking reads

Usage 1:

$bamtyperlinksbamfile.bam1.contig2,[contig1,39,SE,69]contig1,[contig2,39,ES,69]impliesalayoutwhichlookslike:---1-->69bp---2-->2.contig3,[contig2,3,SS,58]contig2,[contig3,3,SS,58],[contig1,4,EE,45]contig1,[contig2,4,EE,45]impliesalayoutwhichlookslike:---1-->45bp<--2---58bp---3-->Usage2:reportFRAGMENTcoveragetoo!$ bamtyper links bamfile1.bam bamfile2.bam -c

contig3 , [ contig2 , 3 , SS , 58 ]
contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]
contig1 , [ contig2 , 4 , EE , 45 ]
contig3 0.6206 0.5234
contig2 0.6558 0.0123
contig1 0.6523 0.5634

Where:
contig3 0.6206 0.5234

Reports 0.6206 fragments per base in bamfile1 and 0.5234 in bamfile2
If these were 100bp reads then this would imply
coverages of 62x and 52x respectively

# Administration

Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/BamTyper

This software is currently unpublished.

Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.