4.11 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.

4.11.1 Parameters

4.11.1.1 Input

--bam Input_bam_file.bam Input bam file

4.11.2 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.

4.11.3 Usage Example

# Simulate a BAM File with actual quality = 0.9*BaseQuality
atlas simulate --recal "quality:polynomial[0.9]"

# Create Quality Transformation
atlas qualityTransformation --bam ATLAS_simulations.bam