FINEMAP colocalization pipeline

Author: Mike Gloudemans

About

This pipeline fine-maps eQTL and GWAS using FINEMAP, an efficient tool developed by Benner et al.

The colocalization test is performed by multiplying posterior causal probabilities from the eQTL and GWAS studies, to generate a colocalization posterior probability (CLPP),
as described in the 2016 eCAVIAR paper by Hormozdiari et al.

The input files for this pipeline are a GWAS file, an eQTL file, and a reference VCF file (for computing LD; we recommend using a VCF from 1000 Genomes).

Setup

To run this pipeline, first clone this repository into your desired directory.

You will need to install PLINK 1.9 and FINEMAP. Binary executables for these tools must be placed in the /bin directory. The PLINK executable must be named plink and the FINEMAP executable must be named finemap.

IMPORTANT: The current pipeline works only with FINEMAP v1.1, which is not the latest version. In my next release of this pipeline, I do hope to make the scripts compatible regardless of which FINEMAP version is used.

Preparing Input Files

GWAS and eQTL summary statistics

GWAS and eQTL input files must be tab-delimited lists of SNPs, containing at least the following columns:

• chr: Chromosome
• snp_pos: Position of SNP (the GWAS, eQTL, and LD reference VCF files must all be from the same build)
• alt: Effect allele
• ref: Non-effect allele
• beta: Estimated effect size of the alt allele, when compared with the ref allele
• se: Standard error of beta

eQTL files must additionally contain a gene column that specifies which gene's expression is being tested.

The column order does not matter, but they must be specified in the header of the file.

An example GWAS input file:

chr     snp_pos alt     ref     beta        se          pvalue
1       751756  C       T       .013006     .017324     .4528019
1       752566  A       G       -.005243    .0157652    .7394597
1       752721  G       A       -.003032    .0156381    .8462652
1       752894  C       T       .00464      .0162377    .7750657
[...]

Note that it is okay to have additional columns beyond the required ones; these will be ignored when the program is run. What's important is that all the required columns are included.

(Note: For the eQTL files, a chi-squared test statistic can be specified under a chisq column as an alternative to the beta and se columns.)

The GWAS, eQTL, and VCF files must be sorted first by chromosome and then by snp position, and finally zipped with bgzip and indexed using tabix. This ensures that the pipeline will run at a reasonable speed.

The following two commands could be used to index a file named my_eqtl_file.txt with the chromosome number in the second column (corresponds to -s parameter) and the chromosome position in the third column (-b and -e parameters):

bgzip -f /home/my_eqtl_file.txt
tabix -f -S 1 -s 2 -b 3 -e 3 /home/my_eqtl_file.txt.gz

Reference VCF

FINEMAP requires a reference VCF to compute the LD between positions of interest.

We recommend using the 1000 Genomes VCF, which can be obtained freely from the 1000 Genomes website.

Running the Pipeline

To run the pipeline, you must specify the input files, the reference genome, and the number of individuals in the reference genome. You must also specify a SNP position of interest; the pipeline will analyze all SNPs near this reference SNP. Currently, SNPs on the sex chromosomes are not supported.

By default, the pipeline will test for colocalization with every gene that has eQTLs in the region. To limit analysis to a single gene, modify the gene parameter as described below in the "optional parameters" section.

The required parameters are chrom, snp_pos, eqtl_file, gwas_file, vcf_file, and N.

• chrom: chromosome of reference SNP of interest
• snp_pos: position of reference SNP of interest
• eqtl_file: bgzipped and tabixed eQTL summary statistics file
• gwas_file: bgzipped and tabixed GWAS summary statistics file
• vcf_file: bgzipped and tabixed reference genome VCF, for computing LD
• N: number of individuals in the reference genome

The vcf_file parameter can be modified to accommodate separate files for each chromosome. i.e. If the name of the VCF for chromosome is chr1.vcf.gz, then you can input chr{0}.vcf.gz and the script will substitute the appropriate chromosome number as necessary.

Example:

The following command would test for colocalization between gwas.txt.gz and eQTLs for all genes in eqtl.txt.gz that are near the position chr1:10000000. LD between SNPs would be computed using 1000genomes.chr{0}.vcf.gz, which includes 2504 individuals.

python ./dispatch.py -g gwas.txt.gz -e eqtls.txt.gz -v 1000genomes.chr{0}.vcf.gz \
            -N 2504 -c 1 -s 10000000

Optional parameters:

• gene: limit analysis to this gene only
• eqtl_format: can be one of three values: [effect_size, chisq, tstat]. The default value is effect_size, which will be used for most eQTL studies. eQTLs called using RASQUAL may instead report chi-squared statistics, which requires use of the chisq option. In this case, the eQTL summary statistics file must have a chisq column but does not require beta and se.
• gwas_format: can be one of three values: [effect_size, log_odds_ratio, pval_only]. The default value is effect_size. log_odds_ratio allows the beta column to be replaced with a column labeled log_or. pval_only requires a pvalue column; with this option the beta and se columns may be omitted.
• window: number of bp to analyze in either direction from the reference SNP. Default value is 500000. Large values (>1MB) may take significantly longer to run.

Viewing Results

The results of the pipeline are placed in a time-stamped folder in the output directory.

At the top level, the directory contains a file [gwas_name]_finemap_clpp_status.txt. This file contains a row for each locus tested. The sixth column is the CLPP score. For more information on interpreting the CLPP score, see Hormozdiari et al. We suggest filtering tested loci by the CLPP score and then visualizing the locus for further confirmation, to avoid false positives.

A good starting filter is to select loci with at least 100 variants tested, a CLPP score of > 0.02, and a top -log(pvalue) of > 5 for both the eQTL and the GWAS studies. These filters can be made more stringent as needed if too many false positives are being detected.

"Rainbow" visualizations of the tested loci are available in the plots subdirectory. Each locus contains one scatterplot showing eQTL significance vs. GWAS significance, and a double Manhattan plot showing the significance of each SNP for the GWAS study on top and the eQTL study on the bottom. Each SNP is colored the same in all three of the plots. However, the colors provide only information about physical distance in base pairs; no information is given about LD. To visualize LD, we recommend instead using a tool like LocusZoom.

The finemap directory contains two file for each colocalization test, showing the posterior causal probabilities for each SNP at the locus. These probabilities are shown in the snp_prob column.