Hi Loic,
Thank you again for the wonderful session yesterday.
I have a question about heritability. When we have a large sample size, is it standard practice to use PLINK to estimate SNP-heritability in a set of unrelated individuals, or would you normally recommend another tool (e.g. GCTA/BOLT, etc.) for this step?
I also had a related question about alleles in PLINK. I know you did not cover PLINK in the session, but could you briefly explain (or point me to a resource on) how to obtain or define the REF/ALT alleles and the effect allele when working with PLINK genotype data (i.e. bed/bim/fam files)? Do the genotype company provide that information using a ref panel?
Thanks
Shalini