yuxinyuanqt/metastaar_notebook_terra

Notebook Script for MetaSTAAR in Terra

metastaar_notebook_terra

Notebook Script for MetaSTAAR in Terra.

Description

These are the notebook scripts for rare variant meta-analysis of WGS data based on the Meta-analysis of variant-Set Test for Association using Annotation infoRmation (MetaSTAAR) method, including (1) generating summary statistics of rare variants (RVs) and (2) performing rare variant meta-analysis.

Usage

Container image: zilinli/metastaar_dockerimage_terra_notebook.

MetaSTAARWorker_Cov_Generation.R and MetaSTAAR_Wroker_Score_Generation.R are the notebook scripts for generating summary statistics of rare variants based on MetaSTAARWorker.
Specifically, MetaSTAARWorker_Cov_Generation.R is used to generate the sparse weighted linkage disequilibrium (LD) matrices. MetaSTAARWorker_Score_Generation.R is used to generate the individual variant summary statistics of all variants across the genome.

MetaSTAAR_RVAT_Sliding_Window.R and MetaSTAAR_Individual_Analysis.R are the notebook scripts for performing rare variant meta-analysis using the summary statistics generated by MetaSTAARWorker. Specifically, MetaSTAAR_RVAT_Sliding_Window.R is used to perform sliding window analysis across the genome. MetaSTAAR_Individual_Analysis.R is used to perform individual analysis of common variants across the genome.

For the access of TOPMed aGDS files in Terra, please send an email to [email protected] for access. TOPMed Freeze 5 aGDS files are in the workspace "MetaSTAAR_Lipids_F8". TOPMed Freeze 8 aGDS files are in the workspace "topmed_agds".

Computation Cost

MetaSTAARWorker_Estimated_Cost.pdf is the benchmarked cost of MetaSTAARWorker in Terra.