Getting FASTA output from PLINK files using Biopython

Here is a bit of code that you can use to extract FASTA files from PLINK genotype calls. I am doing a few assumptions: There is a reference genome to compare against If no data is available from the genotyping we will infer the reference call. This might be acceptable for some Whole Genome Sequencing data sources (and even so…), but if you are using something less dense then you might want to mark it as missing data.


#Bioinformatics #Python