Allele_frequency_federation

This repository contains scripts that can be used to compute the allele frequencies using data generated in small cohorts.

Download and running steps

The folowing instructions are for Windows users

Install python with required packages

Download and install python - https://www.python.org/downloads/windows/

Download and install numpy - "pip install numpy" in the command line, ie CMD terminal

Download and install pandas - "pip install pandas" in the command line

Download the scripts

Fill the samples_to_aggregate file

This should contain the folders and the names of the files on whiich partial MAF should be determined. If a file contains several samples, these need to be specified in the samples field (";" separated)

Run

python genomes_to_maf.py --samples_file [samples_to_aggregate.xls] --destination [destination folder]

*replace [name] with the name of the file