4.10 trimSoftClips

Removing soft clipped bases from reads

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

4.10.1 Input

Required inputs :

--bam Input_bam_file.bam

Input bam file

Optional inputs :

--pmd "library_type:model_for_5'_read:model_for_3'_read" or --RGInfo

Library type followed by the model to be used for the 5-prime read-end and the 3-prime read-end which can be either “Exponential” or “Empiric”. All three arguments must be provided as a string, divided by colons (:). e.g. : –pmdModels “doubleStrand:Exponential:Exponential”. Used to specify Post-mortem damage parameters. Can also be provided as a .txt file (see PMDfor generating such a file). Default = Will assume there is no PMD in the data.

--recal recal_model or --RGInfo

A common recal model for all read groups. Used to specify Quality score recalibration parameters. Can also be provided as a .txt file (see recal for further information). Default = ‘-’, no recalibration is performed.

Specific Parameters :

--outQual integer_1,integer_2	to constrain the quality scores to the indicated range (inclusive) when writing alignments. Default = uses the full range of quality scores when writing alignments.
--writeBinnedQualities	To write Illumina-binned quality scores. Default = Will write raw quality scores

• See Filter parameters to apply specific filters for bases, reads and parsing window setting.

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

4.10.2 Output

*_softClippedBasesRemoved.bam	BAM file containing alignments after soft-clip trimming.
*__softClippedBasesRemoved.bam.bai	Index file for BAM file containing alignments after soft-clip trimming.
*_filterSummary.txt	File contatining Filter summary of general filter counts.
*_RGInfo.json	File containing read group info.

4.10.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 277

out="trimSoftClips"
$atlas --task trimSoftClips --bam simulate.bam \
       --fixedSeed 270 --out $out --logFile $out.out 2> $out.eout

for f in *.bam; do
    out=${f%.bam}
    $atlas --task assessSoftClipping --bam $f \
           --fixedSeed 271 --out $out --logFile $out.out 2> $out.eout
done