coloc

NB! Not a polished product. A workflow for running colocalisation analysis on eQTL vs pQTL or eQTL vs GWAS data. The analyses performed are CLPP (colocalisation posterior probability), coloc.abf (here referred to as coloc v3) and coloc.susie (here referred to as coloc v5). To run the workflow, submit run_pqtl.sh or run_gwas to HPC.

Usage

Input parameters:

• --eqtl_tsv TSV file with 6 columns. Example in sample_data/sample_eqtl.tsv.
• eqtl_dataset_id Dataset name or identifier.
• eqtl_sumstats Summary statistics file containing the following columns: molecular_trait_id, chromosome, position, ref, alt, variant, ma_samples, maf, pvalue, beta, se, type, ac, an, r2, molecular_trait_object_id, gene_id, median_tpm, rsid
• eqtl_sumstats_index Tabix-generated index file for the summary statistics file.
• eqtl_permuted Permutation file containing the following columns: molecular_trait_object_id, molecular_trait_id, n_traits, n_variants, variant, chromosome, position, pvalue, beta, p_perm, p_beta
• eqtl_credible_sets Credible sets file containing the following columns: molecular_trait_id, gene_id, cs_id, variant, rsid, cs_size, pip, pvalue, beta, se, z, cs_min_r2, region
• eqtl_lbf LBF variable file containing the following columns: molecular_trait_id, region, variant, chromosome, position, lbf_variable1, lbf_variable2, lbf_variable3, lbf_variable4, lbf_variable5, lbf_variable6, lbf_variable7, lbf_variable8, lbf_variable9, lbf_variable10
• --pqtl_tsv (only for run_pqtl.sh). TSV file formatted exactly like eqtl_tsv, only the prefix changes from "eqtl" to "pqtl". Example in sample_data/sample_pqtl.tsv`.
• --gwas_tsv (only for run_gwas.sh). TSV file with 5 columns. Example in sample_data/sample_gwas.tsv.
• gwas_subset Subset name or identifier.
• gwas_clpp TSV file containing the following columns: molecular_trait_id, region, variant, chromosome, position, ref, alt, cs_id, cs_index, pip, z, cs_min_r2
• gwas_coloc3 TSV file containing the following columns: molecular_trait_id, region, variant, ref, alt, chromosome, position, maf, beta, se, an, ac, n, log10p, info
• gwas_coloc5 TSV file containing the following columns: molecular_trait_id, region, variant, chromosome, position, lbf_variable1, lbf_variable2, lbf_variable3, lbf_variable4, lbf_variable5, lbf_variable6, lbf_variable7, lbf_variable8, lbf_variable9, lbf_variable10
• --chromosomes comma-separated list of chromosomes.
• --n_chromosomes number of chromosomes in previous list
• --chr_batches number of splits to create for each chromosome (1 would analyse the entire chromosome, 3 would split each chromosome into 3 different jobs).
• --metadata_file File to use for reference file creation. Examples
• --outdir Directory to write the results to.

Bioinformatics example

1. Download necessary files by navigating to bioinformatics_example/bioinformatics_data and running sbatch download_data.sh in the terminal (takes a while).
2. Navigate to main folder, start workflow execution from terminal with the command sbatch run_bioinformatics_gwas.sh or sbatch run_bioinformatics_pqtl.sh
3. The results will appear in results_bioinformatics_gwas or results_bioinformatics_pqtl, respectively.