6.10 saf

Estimating Site Allele Frequencies {#saf}

6.10.1 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

6.10.2 Output

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

6.10.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --type SFS --theta 0.001 --fixedSeed 212 \
  --chrLength 15111 --depth 11 --ploidy 2 --sampleSize 1

name="GLF"
samples=""
for f in *.bam; do
    out=${f%.bam}
    $atlas --task GLF --bam $f  \
       --fixedSeed 215 --out $out --logFile $out.out 2> $out.eout
    samples="${samples}$out.glf.gz,"
done

out="saf"
$atlas --task saf --glf $samples --fasta simulate.fasta \
       --fixedSeed 219 --out $out --logFile $out.out 2> $out.eout