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BETASEQ: A Powerful Novel Method to Control Type-I Error Inflation in Partially Sequenced Data for Rare Variant Association Testing

BETASEQ is a powerful method to control Type-I error inflation in partially sequenced data for rare variant association testing. BETASEQ is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. BETASEQ can work with any existing rare variant association methods that use genotypes or imputed genotypes as input. The current version is a pre-release. For details, please refer to our tutorial.

Comments and suggestions are welcome, please e-mail Song Yan at or Yun Li at