Overview

Write read information (first or second mate, forward or reverse mapping, ...) to file for every site.

Input

• A BAM file

Output

A text file with the following columns:

• chr
• pos
• depth
• numA: number of A's
• numC: number of C's
• numG: number of G's
• numT: number of T's
• numAlleles: number of different alleles
• numFirstMate: number of reads that are first mates
• numSecondMates: number of reads that are second mates
• numFwd: number of forward mapping reads
• numRev: number of reverse mappint reads

Usage Example

.. sourcecode:: bash

./atlas task=mateInfo bam=example.bam

Engine Parameters

Engine parameters that are common to all tasks can be found here <https://bitbucket.org/WegmannLab/atlas/wiki/Engine%20Parameters>_. This task accepts the parameters specific to windows.