Note: This repository collects scripts for CADRE and CHARGE joint project that aims to conduct association analyses of Alzheimer’s Disease (AD) by using ADSP 17K whole genome sequence (WGS) data which is NIAGADS R3 release.

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Project Files Description

Input file

• Bi-allelic QC VCFs (one VCF for a autosomal) with 16,905 samples released in October 2021
• Multi-allelic VCFs (one VCF for a autosomal) with 16,906 samples released in March 2021
• Phenotype file

Output file

• VCFs (one VCF for a autosomal) with sample and variant filtering done
• Summary csv files of association analyses

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Steps

1. VCF preparation README
2. Single-variant association analysis for variant with MAF > 0.5% README
3. association analysis for rare coding or non-coding variants with MAF < 1% using STAAR README

Dependencies

Tools

• HTS library v1.12 (has embedded in libs)
• bcftools v1.12 (has embedded in libs)

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License

The implementation is available for academic and nonprofit use for free LICENSE.md.

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Contacts

Wan-Ping Lee - Email, Research Assistant Professor | Associate Director for IT of NIAGADS, Department of Pathology and Laboratory Medicine, University of Pennsylvania

Gina Marie Peloso - Email, Associate Professor, Department of Biostatistics, Boston University

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Acknowledgments