Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
0
0
Entering edit mode
1 day ago
Mllepnos • 0

I am relatively new to bioinformatics and 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! :)

PLINK LiftOver PLINK2 BED GWAS • 78 views
ADD COMMENT

Login before adding your answer.

Traffic: 1605 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6