Hi, I have coordinates in bed format and i am interested to associate SNP with the segments. I looked at plink format but here data is in tsv format. I tried to convert tsv format to bed format but there are multi-SNP haplotypes or SNP-SNP interactions. (Here is sample file link) "GWAS Sample File.tsv"
The sample file was prepared from GWAS catalog. https://www.ebi.ac.uk/gwas/
The column no 12 "CHR_ID" and 13 "CHR_POS" contains different SNP positions for same phenotype. I want to split this info for each SNP on each line. Is there any possible way?
How can i process GWAS data? Is there any tool available to search multiple SNPS on bash?
Thanks in advance.
Muhammad Shahbaz Munir