Software

Github (gootga)

MAGON:

This is a pyhton script that filters eigenstart by population. Given a list in plain text format (one column) with names of populations the script will search the input.ind and filter the input.geno accordingly. It will output an new output.ind and output.geno with only the individuals that belong to the populations in the list provided. In the default script example the extension for the population list is .dict but any .txt file is valid.

https://github.com/gootga/MAGON

HYBSIM:

This is a pyhton script to simulate hybrid genomes/genotypes between two single paretal genotypes (two individuals) in eigenstrat format. The script follows probabilistic mendelian logic for the offspring. Missing data (9) in one or both of the parental sources is translated into the offspring genotype as missing data too. So beware, offspring accumulates missingness rate from both parents.

https://github.com/gootga/HYBSIM