A small python tool to calculate pairwise mismatch rate between all individuals in an EigenStrat dataset.
Mathematical equations added to README using this tool.
usage: pMMRCalculator.py [-h] [-i <INPUT FILES PREFIX>] [-o <OUTPUT FILE>]
[-s <INPUT FILES SUFFIX>] [-v] [-j]
Calculate the pairwise mismatch rate of genotyped between all individuals in
the input eigenstrat dataset.
Available options:
-h, --help show this help message and exit
-i <INPUT FILES PREFIX>, --Input <INPUT FILES PREFIX>
The desired input file prefix. Input files are assumed
to be <INPUT PREFIX>.geno, <INPUT PREFIX>.snp and
<INPUT PREFIX>.ind .
-o <OUTPUT FILE>, --Output <OUTPUT FILE>
The desired output file name. Omit to print to stdout.
-s <INPUT FILES SUFFIX>, --Suffix <INPUT FILES SUFFIX>
The desired input file suffix. Input files are assumed
to be <INPUT PREFIX>.geno<INPUT SUFFIX>, <INPUT
PREFIX>.snp<INPUT SUFFIX> and <INPUT PREFIX>.ind<INPUT
SUFFIX> .
-v, --version Print the version of the script and exit.
-j, --json Create additional json formatted output file named
<OUTPUT FILE>.json . [Default:
'pmmrcalculator_output.json']
pMMRCalculator.py -i test.input -o test.output.txtInd1 Ind2 nSNPs nMismatch pMismatch
Indiviudal1 Individual2 585385 137736.0 0.23529
Indiviudal1 Individual3 585199 140524.5 0.24013
Indiviudal1 Individual4 584162 140474.0 0.24047
Indiviudal2 Individual3 583507 140741.5 0.24120
Indiviudal2 Individual4 586613 141040.0 0.24043
Indiviudal3 Individual4 586005 140373.0 0.23954
The output will include a header and five coloumns. These columns contain the ID of the two individuals in each pairwise comparison, the number of overlapping SNPs between the two individuals, the cumulative mismatch proportions across all SNPs, and the pairwise mismatch rate between the individuals.
The number of overlapping SNPs (nSNPs) shown here corresponds to the
intersection of non-missing genotypes of the two individuals.
The cumulative mismatch proportions are calculated with the following formula:
Where GiS is the genotype of individual i at SNP S, and GjS is the genotype of individual j at SNP S.