# ATLAS / Auxiliary Tools: assessSoftClipping

## Overview

This tool provides soft clipping statistics for all reads, i.e. the number of soft-clipped positions and their bases.

## Output

a txt file with suffix _clippingStats.txt.gz with the following information:

• read name
• mapping position of read
• number of softclipped bases on the left side of the read
• number of bases that were not softclipped per read
• number of softclipped bases on the right side of the read

if the option printSequences is used, the sequences underlying these statistics are also written to file.

## Usage Example

./atlas task=assessSoftClipping bam=example.bam printSequences


## Specific Arguments

• printAll: Write softclipping stats for all alignments to file, also those that do not have any softclipping
• printSequences: Write softclipped sequences to file

## Engine Parameters

Engine parameters that are common to all tasks can be found here.

Updated