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saigegit committed May 19, 2022
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Expand Up @@ -13,12 +13,12 @@ This documentation describes how to perform the exome-wide association tests wit

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[Prerequisites](#prerequisites)
[Save SAIGE image to DNAnexus](#save-saige-image-to-dnanexus)
[Step 0: constructing a sparse GRM using the LD pruned hard-called genotypes.](#step-0-constructing-a-sparse-grm-using-the-ld-pruned-hard-called-genotypes)
[Step 1: fitting the null linear/logistic mixed model using the sparse GRM and estimating variance ratios](#step-1-fitting-the-null-linearlogistic-mixed-model-using-the-sparse-grm-and-estimating-variance-ratios)
[Step 2: Performing exome-wide gene-based tests](#step-2-performing-exome-wide-gene-based-tests)
[Benchmark on the cost for jobs on DNAnexus](#benchmark-on-the-cost-for-jobs-on-dnanexus)
- [Prerequisites](#prerequisites)
- [Save SAIGE image to DNAnexus](#save-saige-image-to-dnanexus)
- [Step 0: constructing a sparse GRM using the LD pruned hard-called genotypes.](#step-0-constructing-a-sparse-grm-using-the-ld-pruned-hard-called-genotypes)
- [Step 1: fitting the null linear/logistic mixed model using the sparse GRM and estimating variance ratios](#step-1-fitting-the-null-linearlogistic-mixed-model-using-the-sparse-grm-and-estimating-variance-ratios)
- [Step 2: Performing exome-wide gene-based tests](#step-2-performing-exome-wide-gene-based-tests)
- [Benchmark on the cost for jobs on DNAnexus](#benchmark-on-the-cost-for-jobs-on-dnanexus)

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