I am learning to do GWAS analysis in Arabidopsis. I used some accessions from the 1135 list (1001 genomes project)for a GWAS experiment. I have some questions about the genotype data. I find there are several different genomes data including .vcf format and .hdf5 format. I selected the one named “1001_SNP_MATRIX.tar.gz”. So I want to ask if it is the right genotype data for GWAS analysis?. And also I have a problem converting the hdf5 format to STRUCTURE format. Does anybody know how to import this SNP matrix into the STRUCTURE software?. Look forward to your reply.
Thanks and Regards