Overview

Each folder here has the following format:

• <run_order_number>_<description_of_what_is_done>/

Each folder has the following subfolders, each with their own README.md:

• code/
• input/
• output/

Please see the individual subfolder README.md files for further information.

Folder summaries

00_prep_inputs_for_metaxcan/

• This folder prepares raw GWAS information for MetaXcan's SPrediXcan process.
• This includes METAL, GWAS parsing, and summary imputation to variants used in predictdb.org's GTEX V8 mashr models.

010_ukb_bcac_meta_new_loci/

• This folder contains a GWAS analysis of the meta-analysis of UKB/BCAC for overall breast cancer to find newly identified GWAS variants.

01_spredixcan_eqtl_sqtl/

• This folder contains the SPrediXcan related code/input/output.

02_acat_eqtl_sqtl

• Contains the ACAT (p-value combination method) results.

03_enloc/

• Finemapping enloc.

04_cojo_ctwas/

• Contains conditional joint analysis (COJO) and the subsequent conditional TWAS (CTWAS) based on the COJO results.
• Due to computational strain only Bonferroni significant variants from each study are run through the COJO/CTWAS process.

05_focus:

• Contains Bogdan Lab's FOCUS resuls for our studies of interest.

08_expression_pred_ccv:

• Contains code/input/output pertaining to the enrichment of credible causal variant (CCVs), made recently to address AJHG reviewer comments.

999_reporting_friendly_tables:

• Contains precursor tables to those final tables presented in the paper. Convenient files for genetic distances, gencode 26 to 40 conversion, are included.