Hello, this is my first post in this renowned group. Acutally, I am struggling with Haplotype based GWAS. I am doing GWAS on a plant pathogen. The single SNP GWAS has yielded any significant result. So, I have decided to use Haplotype based GWAS. I have a VCF file containing 717045 SNPs. I used Plink to generate haplotype blocks. It has yielded more than 74000 haplotype blocks. But I do not know how to use that data in the GWAS. From the plink output, the data is in .blocks or .blocks.det format.
Can someone please give me some ideas about how to use that data for GWAS? or How can I perform a Haplotype Based GWAS? Using which tool?
Looking forward to your reply. Thank you very much.
Regards Anik Dutta