6.1 alleleCounts

Estimating population allele counts

This task estimates the most likely allele count from a multi-sample VCF containing bi-allelic sites. Such a VCF file can be created with the ATLAS task majorMinor. The method is based on Nielsen et al. (2012) PLoS One.

6.1.1 Parameters

6.1.1.1 Input

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

Optional

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

Example text file:

SAMPLE POPULATION
sample1 1
sample2 1
sample5 2
sample8 2

6.1.1.2 Specific

Parameter Description Default
--dosaf Write the sample allele count likelihoods to alleleCountsLKs file. This file is not written.
--reportFreq freq Specify after how many lines the reading progress is printed to the terminal. 10000
--transform Transform the format of an existing file, can be set to default,withAlleles,treemix or flink default
--outFormat Choose the format of the output files, avalaible : withAlleles, treemix, flink default

Output

*_alleleCounts.txt.gz A zipped text file containing the MLE allele counts for all positions and populations.
*_alleleCountsLKs.txt.gz A zipped text file containing the log likelihoods of MLE allele counts for all positions and populations.

Usage Example

atlas --task alleleCounts --vcf ATLAS_simulations.vcf.gz --fixedSeed 0 --out alleleCounts --logFile alleleCounts.out
atlas --task alleleCounts --dosaf --vcf ATLAS_simulations.vcf.gz --fixedSeed 0 --out alleleCountsSAF --logFile alleleCountsSAF.out
atlas --task alleleCounts --transform alleleCounts_alleleCounts.txt.gz --fixedSeed 0 --out transform --logFile transform.out