Cow genetic analysis

Here are the details needed for reproducing the genetic similarity data between cows in the research, by using SNPs genetic data provided as a basis:

when working with FWASS (see paper methods):

Code for creating the genetic similarity matrix: \texttt{python3 compute_similarity.py -i INPUT_FILE.vcf --weighted --ns -o OUTPUT_FILE}

the “--weighted” flag calculates an allele frequency-weighted metric the “—ns” flag converts the output into a format that is compatible with the input format required for Netstruct Hierarchy (.txt file)

Source: https://github.com/Greenbaum-Lab/FWASS.git

See https://github.com/Greenbaum-Lab/FWASS for further details.