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 Input

Required inputs :

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

Optional inputs :

  • None

Specific Parameters :

  • None

6.8.2 Output

Printed to screen The columns are: chromosome, position, maximum 16bit-phred scaled genotype likelihood, depth, RMS mapping quality, the 10 16bit-phred scaled genotype likelihoods

6.8.3 Usage Example

#! /bin/bash

# Set atlas path
atlas=$(dirname "$0")/../build/atlas

# Simulate a BAM File
$atlas simulate --logFile simulate.out

# Create GLF File
$atlas GLF --bam ATLAS_simulations.bam --logFile GLF.out

# Create txt-glf-file
$atlas printGLF --glf ATLAS_simulations.glf.gz --logFile printGLF.out