GCTA grm

[wangzeng2001]

Hi,Zhou!
I read your article on the tomato pan-genome, fantastic job! But I get confused when I read your method section about genome-wide association study, you said that "After pruning using PLINK (v.2.0) with the parameter ‘-indep-pairwise’ set to ‘50 5 0.2’, the pruned SNPs were used for the kinship matrix (genetic relationship matrix; GRM). For SNPs and indels, the pruned dataset (-indep-pairwise 100, 1, 0.98) was used". Does this sentence mean that the second parameter is used when the sum of snp and indel is in the vcf file? I see that your article also includes other types, sv and indel separately, or SNP+indel+SV, does this need to filter the LD, what parameters do you use?
Sorry to bother u. Thanks a million!

[YaoZhou89]

The first is used to construct the GRM for LOCO-GWAS, and the latter for heritability estimation.