4.8 qualityTransformation

Printing Quality Transformation

qualityTransformation allows you to track how the base quality scores are transformed by recalibration (either BQSR or recal). Specifically, you can make pairwise comparisons between two sets of quality scores:

  • the original quality scores versus those obtained through BQSR or recal recalibration
  • the quality scores resulting from BQSR versus those resulting from a run of recal
  • the quality scores resulting from two different runs of recal, e.g. one performed using the X chromosome and one performed using mitochondrial DNA

The log file reports the R squared, which represents the correlation between the two sets of quality scores.

4.8.1 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 :

  • 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.

4.8.2 Output

*_RGInfo.json File containing read group info.
*_SimReadGroup1_qualityTransformation.txt File containing quality transformation for each read group.
*_qualityTransformation.txt File containing quality transformation of total data.
*_filterSummary.txt File containing Filter summary of general filter counts.

4.8.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 199

out="qualityTransformation"
$atlas --task qualityTransformation --bam simulate.bam \
       --fixedSeed 190 --out $out --logFile $out.out 2> $out.eout