6.9 saf

Estimating Site Allele Frequencies {#saf}

6.9.1 Input

Required inputs :

--glf glf_file1.glf.gz,glf_file2.glf. or --glf glf_file.txt

Input glf files for every sample of the population. Can be provided on the command line or with an input text file (one file name per line).

Example text file:

glf_file_1.glf.gz

glf_file_2.glf.gz

glf_file_3.glf.gz

glf_file_4.glf.gz

Optional inputs :

• None

Specific Parameters :

• None

6.9.2 Output

*_saf.idx	SAF index file.
*_saf.gz	SAF entry file.
*_saf.pos.gz	SAF position file.

6.9.3 Usage Example

#! /bin/bash

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

# Simulate 5 BAM files in Hardy–Weinberg equilibrium
$atlas simulate --type HW --sampleSize 5 --logFile simulate.out

# Create GLF files
for f in *.bam; do
    $atlas GLF --bam $f
done
samples=$(ls -1 *.glf.gz | paste -s -d ',' -)

# Create site allele frequencies file
$atlas saf --glf $samples --fasta ATLAS_simulations.fasta --logFile saf.out