SAIGE-QTL takes three steps to perform cis-eQTL tests for common variants using single-variant tests and two steps for rare/less frequent variants using set-based tests

• step 1 is shared by both common and rare variant tests

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Table of contents

• Step 2 - single variant test (common variants)
• Step 3 - gene p-values (common variants)
• Step 2 - set-based tests (rare variants)