Overview

This task allows you to write genotype likelihoods to a GLF file, format described here.

Input

• BAM file
• optional: quality score recalibration file
• optional: post-mortem damage parameters

Output

• glf.gz binary file

Usage Example

./atlas task=GLF bam=example.bam recal=example_recalibrationEM.txt pmdFile=example_PMD_input_Empiric.txt

Specific Arguments

• printAll: print likelihoods for all sites, even those without data

Engine Parameters

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