Understanding SNP Coordinates for .bed File Creation

Question

[iarmir]

Hello! I need some guidance on creating a .bed file for filtering my VCF data based on the positions of two SNPs (rs3730025 and rs56394458). I want to check for the presence of these SNPs in my patients.

For rs3730025, the position is chr17:63480412. Could someone clarify whether the .bed file should have the start and end both marked as 63480412, OR should the start be 63480412 and the end 63480413 (+1)?

Similarly, for rs56394458 with the position chr17:63481680, I have the same question. Thanks in advance for your help!

[Pierre Lindenbaum]

Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems