This pipeline performs transcriptome-wide association analysis using PTWAS software.
Required inputs are:
-
gwas_summary_stats: GWAS single-SNP z-scores in a bgzipped vcf file.
-
ld_reference_panel: consists of a set of vcf files used for computing LD information. Default = 1000 Genomes project (phase 3 version 5).
- eqtl_weights: used by PTWAS scan procedure to construct composite IVs, also known as the eQTL weights for burden test. Pre-computed weights file from 49 tissues in the GTEx project are used by default.
http://sashagusev.github.io/2017-10/twas-vulnerabilities.html