Differences between BED and bed files

Question

[naz]

Hello,

I am very new to bioinformatics and I apologize if this question is simple/obvious.

My goal is to perform a polygenic risk score analysis however I am having trouble with the preprocessing of my data.

I downloaded a dataset with FAM, BIM, and BED files. I want to use plink to convert these files to a PED file however I believe the .BED file is a Browser Extensible Data as seen in the UCSC FAQ (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) and not the desired .bed (PLINK 1 binary biallelic genotype table).

My questions are;

1. How can you distinguish between these two file formats? Is it simply the capitalization of the suffix .bed vs .BED?

2. What tools can I use to convert the BED/FAM/BIM files to the desired PED file format?

Answer 1

[Istvan Albert]

The two-bed formats UCSC BED and Plink BED are unrelated and cannot be used interchangeably. It is unfortunate that both are named the same.

The capitalization may help you remember which is which.

Use plink to convert your files, there are other tools as well, but as far as I know plink can convert them as well.