6.9 printGLF

Printing a GLF file to screen

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

6.9.1 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

6.9.2 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

6.9.3 Usage Example

#! /bin/bash

# `--fixedSeed = N` is needed to have reproducable results in regression test

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 4321

out="GLF"
$atlas --task GLF --bam simulate.bam \
       --fixedSeed 321 --out $out --logFile $out.out 2> $out.eout

out="printGLF"
$atlas --task printGLF --glf GLF.glf.gz \
       --fixedSeed 3 --out $out --logFile $out.out 2> $out.eout \
       | tail -n +14 | head -n -4 > GLF.txt