No known loci for conditional analysis? about staarpipeline-tutorial HOT 1 CLOSED

Hi Daniel,

Thanks for your questions. For analytical follow-ups in STAARpipeline, the known loci refer to a list of variants that are known to be associated with the trait of your interest, either reported in previous literature (e.g. GWAS catalog) or the individual (single-variant) analysis of the current study or both. The goal of adjusting for the known loci in the conditional analysis is to dissect rare variant associations independent of known variants. Given such, there is no issue if you don't provide known loci in STAARpipelineSummary, meaning there might not be any previously known genetic variants associated with the trait of interest. Thus, the conditional association strength is the same as the unconditional analysis.

Because STAARpipeline enables functionally-informed phenotype-genotype association analysis, one of the follow-up analyses is to query the functional annotations for all (rare) variants in the significant variant set and identify variant(s) that have a functional impact in driving the association of the set.

I hope this helps.

Best,
Xihao

from staarpipeline-tutorial.