6.3 ancestralAlleles

Writing FASTA-file with ancestral alleles

6.3.1 Input

Required inputs :

--alleleCounts Input_file_alleleCounts.txt.gz	A zipped text file containing the MLE allele counts for all positions and populations.
--fastaIndex Reference_fasta_file.fasta.fai	Index file for the reference genome file.

Optional inputs :

• None

Specific Parameters :

--minorCountMaximum integer_value	To set the maximum count of minor allele. Default = the maximum count of minor allele is set to 0.
--totalCountMinimum integer_value	To set the minimum total allele count. Default = minimum total allele count is set to 0.
--population	.

• See Filter parameters to apply specific filters for bases, reads and parsing window setting.

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

6.3.2 Output

*_ancestralAlleles.fasta.fasta	A fasta file containing ancestral alleles.
*_ancestralAlleles.fasta.fasta.fai	Index file for the fasta file containing ancestral alleles.

6.3.3 Usage Example

#! /bin/bash

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

# Simulate 5 samples in Hardy–Weinberg Equilibrium and write vcf file
$atlas simulate --vcf --type HW --sampleSize 5 --logFile simulate.out

# Create allele-count file with alleles
$atlas alleleCounts --vcf ATLAS_simulations.vcf.gz --outFormat withAlleles --logFile alleleCounts.out

# Create fasta-file with ancetral alleles using the calculated allele counts
$atlas ancestralAlleles --alleleCounts ATLAS_simulations_alleleCounts.txt.gz --logFile ancestralAlleles.out