6.2 alleleFreq

Estimating population allele frequencies

alleleFreq estimates the population allele frequencies from a multi-sample VCF file containing bi-allelic sites. Such a VCF file can be created with the ATLAS task majorMinor.

6.2.1 Parameters

6.2.1.1 Input

--vcf example_majorMinor.vcf.gz Input VCF file generated by ATLAS majorminor task.

Optional

--samples alleleCounts_alleleCounts.txt.gz A zipped text file containing the MLE allele counts for all positions and populations. Used with --compare parameter.
--samples samplesPopulations.txt A user-generated .txt file containing the samples to be used and their population affiliation. Different allele frequency will be estimated for different populations.

Example text file:

SAMPLE POPULATION
sample1 1
sample2 1
sample5 2
sample8 2

6.2.1.2 Specific

Parameter Description Default
--likelihoods Write the sample allele frequency likelihoods to alleleFreqLKs file. This file is not written
--reportFreq freq Specify after how many lines the reading progress is printed to the terminal. 10000
--epsF value epsilon for MCMC algorithm. 0.0000001
--iterations value Maximal number of MCMC iterations. 100000
--proposalFrac value MCMC proposal width. 3
--compare Compare 2 VCF files.

6.2.2 Output

*_alleleFreq.txt.gz A zipped text file containing the allele frequencies for all positions and populations.
*_alleleFreqLikelihoods.txt.gz zipped text file containing the allele frequency log likelihoods for all positions and populations.

6.2.3 Usage Example

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

# Create allele-frequency file
atlas alleleFreq --vcf ATLAS_simulations.vcf.gz