sinarueeger / G2G-EBV-manuscript

G2G analysis on Epstein–Barr virus (EBV)

G2G analysis on EBV

This repository contains all scripts relevant for G2G analysis on Epstein–Barr virus (EBV) in HIV patients. For EBV data preparation, please see gitlab.com/ezlab/vir_var_calling. Results are available here: https://doi.org/10.5281/zenodo.4011995.

Usage

In this order:

1. ./make_1_computation.sh: runs the G2G analysis (= many GWASs).
2. ./make_2_results.sh: extracts top results.
3. ./make_3_genomic_lambda.sh: computes the genomic lambdas for all GWASs.
4. ./make_4_figures_tables.sh: makes figures + tables for report.

Note: All bash files have some parameters to choose in the header.

Dependencies

• FINEMAP v1.3.1
• LDStore v1.1
• PLINK2
• GCTA v1.91.7