5.7 GLF

Writing genotype likelihoods to a GLF file

GLF allows estimating and write marginal genotype likelihoods of the bam files to a GLF file.

5.7.1 Parameters

5.7.1.1 Input

--bam Input_bam_file.bam

Input BAM file.

5.7.1.2 Specific

Parameter	Description	Default
--printAll	print likelihoods for all sites, even those without data	only sites with data are written

5.7.1.3 Engine

• General
• Bases
• Reads
• Sites
• Genome

5.7.2 Output

*.glf.gz

Binary file with genotype likelihood estimates.

5.7.3 Usage Example

# Simulate a BAM File
atlas simulate

# Create GLF File
atlas GLF --bam ATLAS_simulations.bam