Question: Multi-SNP haplotypes in GWAS data
gravatar for shahbazmunir11
2.5 years ago by
shahbazmunir1110 wrote:

​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.

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

Mphil Scholar

snp gwas • 896 views
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