Are there any tools available to measure heritability of a trait in genome-wide sequencing data? Are these measures absolute or can they be combined for different studies measuring different traits to find relative heritability measures?
I may be missing something but heritability as in narrow and broad sense is a measure derived from twin studies, i.e., concordance rates in traits in different and shared shared environments in mono- and dizygotic twins. See below for a good review:
I am not sure that you can derive h^2 and/or H^2 from GWAS data. Are your cases/controls unrelated? Do you have family data? Do you have twin data?
Pay attention to the section of the review that describes brilliantly what heritability actually means. It is often misinterpreted and misrepresented!
As it was pointed out by Darren, you can not estimate the heritability of a trait from GWAS data but you can at least get a lower bound for this measurement. You should take a look at the GCTA tool developed by the group of one of the authors in the review quoted by Darren:
In your question you do say genome-wide sequencing data. I don't think you have the numbers of full genome sequences (yet!) to do this calculations but attainable using genotype (ie GWAS) data.