6.8 printGLF

Printing a GLF file to screen

This task allows you to read the binary GLF files produced by ATLAS task GLF.

6.8.1 Parameters

6.8.1.1 Input

--glf Input_glf_file.glf.gz Input file with estimated marginal genotype likelihoods (see GLF for further information)

6.8.2 Output

*.txt The columns are: chromosome, position, depth, RMS mapping quality, the 10 16bit-phred scaled genotype likelihoods

6.8.3 Usage Example

# Simulate a BAM File
atlas simulate

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

# Create txt-glf-file
atlas printGLF --glf ATLAS_simulations_GLF.glf.gz