I am currently working with PLINK GWAS summary statistics generated using the --glm function. I need to convert them into BED format to perform a liftover using UCSC's Liftover tool, but I am encountering some challenges:
Start and End Positions: PLINK’s --glm output only provides a single position per variant, whereas BED format requires both start and end positions. How should I define the end position, especially for SNPs vs. indels?
Handling Indels: Some indels in my data have varying lengths. Should I use the reference allele length to determine the end coordinate, or is there a standard approach for handling indels in BED format?
Efficient Formatting: What is the best way to convert the --glm output into BED format (e.g., using awk, R, or Python) in a reproducible manner?
Any advice or code snippets would be greatly appreciated! :)
