# ATLAS / splitMerge

## Overview

This task should be run before any consecutive variant discovery or population genetic tool to split single end read groups by length and to merge paired end reads. This task is a combination of tasks splitRGByLength and mergeReads. You need to specify which read groups should be considered for splitting or merging. Others will just be written to the BAM as they are.

## Input

• A BAM file

• blacklist.txt (optional): A txt file with blacklisted read names that should be ignored and just written to file, each on a new line.

• A .txt file :

Example:

## Output

• A BAM file with suffix _mergedReads.bam
• A file listing all reads that were filtered out in the merging process with suffix _ignoredReads.txt.gz

## Usage Example

./atlas task=splitMerge bam=example.bam