6.5 geneticDist

Estimating the genetic distance between individuals**

geneticDist estimates the pairwise distances per genomic window between at least two genomes in glf format. This format can be created with the atlas task glf.

In the first step, the frequencies of nine genotype configurations aa/aa, aa/ab, ab/aa, aa/bb, ab/ab, ab/ac, aa/bc, ab/cc and ab/cd are estimated. The genotype configuration aa/aa e.g. corresponds to a locus where both individuals are homozygous for the same allele and the configuration ab/cc corresponds to a locus where one individual is heterozygous and the other is homozygous for a different allele.

In the second step, these genotype configuration frequencies are multiplied by the user-specified distance weights and summed up to produce the genetic distance. Depending on the genetic distance you want to use, you will give different weights to the genotype configurations.

6.5.1 Distance weights

A comma-separated vector of 9 weights, to be assigned to the genotype configurations in the following order: aa/aa,aa/ab,ab/aa,aa/bb,ab/ab,ab/ac,aa/bc,ab/cc,ab/cd. These weights represent how distant from each other you consider the two genotypes of each genotype configuration to be.

6.5.1.1 Predefined distance types with weights

  • squaredDiff : This distance measure corresponds to the amount of alleles that differ between the genotypes. The distance weights in this case are: 0,1,1,4,0,1,4,4,4.
  • euclidian: This distance measure corresponds to the square root of the squaredDiff. If this measure is used in a metric PCA, the MDS will be the same as a PCA.
  • probMismatch : This distance measure corresponds to the probability that a random allele chosen at a random position differs between two individuals. The distance weights in this case are: 0,0.5,0.5,1,0.5,0.75,1,1,1.

6.5.2 Parameters

6.5.2.1 Input

--glf glf_file1.glf.gz,glf_file2.glf. or glfList.txt At least two glf files

6.5.2.2 Specific Parameters

Parameter Description Default
--distType type_of_distance Set one of the predefined distance types squaredDiff
--distWeights 9xnumeric_values Chose types and weights Predefined depending on type of distance type
--iterations integer_value Set the maximum amount of EM iterations. 100

6.5.3 Output

*_distanceEstimates.txt.gz .txt.gz file with distance estimates for each pair of glf files. The columns correspond to the position of the window, the four base frequencies, the nine genotype configuration frequencies and the genetic distance
*_distanceMatrix.txt .txt file containing genetic distance for each pair of glf files in a matrix form.

6.5.4 Usage Example

# Simulate 2 BAM Files
atlas simulate --sampleSize 2 --chrLength 200000

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

# Calcuate genetic distance between the samples
atlas geneticDist --glf $samples