Extracting SNPs Based on Position Information
Sue
Hi Christopher,
I'm reaching out to seek guidance regarding the extraction of SNPs from VCF files. Currently, I'm dealing with VCF files that contain SNP information tagged with axiom IDs, rather than the standard rs# identifiers. Additionally, I possess a list of target SNPs for genetic risk score analysis, identified by their rs#.
Given this scenario, I'm facing the challenge of not having a reference to match axiom IDs with their corresponding rs# identifiers. Consequently, I'm interested in extracting SNPs based on the positional information of the target SNPs.
To elaborate, my objective is to extract SNPs surrounding the target SNPs using the positional information available in the VCF files. Could you please advise if there is a method to achieve this using either PLINK 1.9 or PLINK 2?
I greatly appreciate your assistance with this matter.
