4.1 assessSoftClipping

Assessing level of soft clipping in BAM file

assessSoftClipping provides soft clipping statistics for all reads, i.e. the number of soft-clipped positions (??, their bases) and the counts of the reads.

4.1.1 Input

Required inputs :

--bam Input_bam_file.bam

Input BAM file.

Optional inputs :

--pmd Input_PMD.txt	post-mortem damage parameters (see PMD for generating such a file)
--recal recal.txt	quality score recalibration file (see recal for further information)

Specific Parameters :

--readGroup

To restrict the analysis to the provided readgroup(s).

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

4.1.2 Output

*_softClippingMatrixBoth.txt	Text file with information about distribution of soft clipping on left and right sides of the read combined.
*_softClippingMatrixLeft.txt	Text file with information about distribution of soft clipping on the left side of the read.
*_softClippingMatrixRight.txt	Text file with information about distribution of soft clipping on the right side of the read.
*_filterSummary.txt	A text file with filter summary.

4.1.3 Usage Example

#! /bin/bash

# Set atlas path
atlas=$(dirname "$0")/../build/atlas

# Simulate a BAM File
$atlas simulate

# Assess softclipped bases
$atlas assessSoftClipping --bam ATLAS_simulations.bam