5.5 GLF

Writing genotype likelihoods to a GLF file

GLF allows estimating and write marginal genotype likelihoods of the bam files to a GLF file (format described here).

5.5.1 Input

Required inputs :

--bam Input_bam_file.bam

Input BAM file.

Optional inputs :

--recal OR --RGInfo sample_RGInfo.json	Quality score recalibration file (see estimateErrors for further information).
--pmd OR --RGInfo sample_RGInfo.json	Post-mortem damage parameters (see estimateErrors for further information).

Specific Parameters :

--printAll

print likelihoods for all sites, even those without data. Default = only sites with data are printed/written.

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

5.5.2 Output

*.glf.gz	Binary file with genotype likelihood estimates.
*_filterSummary.txt	A text file with filter summary.

5.5.3 Usage Example

#! /bin/bash

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

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 1

out="GLF"
$atlas --task GLF --printAll --window 7777 \
       --bam simulate.bam \
       --fixedSeed 2 --out $out --logFile $out.out 2> $out.eout