How to estimate SNP-based heritability?

Question

[anikcropscience]

Hello, I have a SNP dataset with 717044 SNPs and 48 phenotypes from a plant-pathogen interaction. I have done GWAS using GAPIT/TASSEL. Now, I want to estimate SNP-based heritability for each of the trait.

Can anyone please recommend which tools are available for estimating SNP-based heritability? Some links of tutorial would be highly appreciated. Looking forward to the suggestions.

Thanks Anik

Answer 1

[Sam]

You can try to use GCTA if you have the genotype data, and use LDSC if you only got the summary statistics from the GWAS. Alternatively, you can also use LDAK. All these software has their own website with some level of tutorial in it.

[anikcropscience]

Thank you very much. I will check those tools.