Publication: Wingo et al., Multi-ancestry brain pQTL fine-mapping and integration with genome-wide association studies of 21 neurologic and psychiatric conditions
This repository provides transparency for critical analysis details of the manuscript.
For MESuSiE analysis notes were collated with minimal editing and shared as:
MESuSiE_notes.txt with scripts shared in
./MESuSiE.
For converting genomic mapping to a jointly VCF dataset, we followed the
approach in pecaller using
samstools to generate mpileup files used as input for
mpileup_to_pileup2. Variant calling, Quality Control & Site Selection,
Cross-Batch Merging, and Final Integration steps were followed using default
values with final quality control parameters given in the manuscript.
Code was tidied for readability using perltidy, prettier, shfmt, and styler.