Güngör Budak's Blog

Bioinformatics, web programming, coding in general

How to Convert PED to FASTA

You may need the conversion of PED files to FASTA format in your studies for further analyses. Use below script for this purpose.

PED to FASTA converter on GitHub

Gets first 6 columns of each line as header line and the rest as the sequence replacing 0s with Ns and organizes it into a FASTA file.

Note 0s are for missing nucleotides defined by default in PLINK

How to run:

perl ped2fasta.pl "C:\path\to\PED_File"