Wrapper scripts for Verena's (yet unnamed) GWAS co-localisation methods
# Install dependencies into isolated environment
conda env create -n vloc --file environment.yaml
# Activate environment
source activate vloc
The wrapper will run 1D-finemapping if only --left_sumstats dataset is specified. If a second dataset --right_sumstats is specified, it will also run 1D-finemapping for the right dataset, followed by co-localisation between the left and right datasets.
If no options are set for --right_* args, they will inherit the equivalent --left_* arg (except for --right_sumstats).
The covariance matrix and meta data (--left_cov and --left_covmeta) are outputs from LDstore. See test_script.sh for example workflow for a single locus.
$ python scripts/vloc.py --help
usage: vloc.py [-h] --left_sumstats <file> --left_cov <file> --left_covmeta
<file> --range <str> [--right_sumstats <file>]
[--right_cov <file>] [--right_covmeta <file>] --outprefix <str>
[--left_kmax <int>] [--left_kstart <int>] [--right_kmax <int>]
[--right_kstart <int>] [--v_scale <float>] [--maxiter <int>]
[--prior <str>] [--g <str>] [--sep <str>]
[--left_rsidcol <str>] [--left_chromcol <str>]
[--left_poscol <str>] [--left_betacol <str>]
[--left_secol <str>] [--left_effalcol <str>]
[--left_ncol <str>] [--right_rsidcol <str>]
[--right_chromcol <str>] [--right_poscol <str>]
[--right_betacol <str>] [--right_secol <str>]
[--right_effalcol <str>] [--right_ncol <str>]
optional arguments:
-h, --help show this help message and exit
input file arguments:
--range <str> Genomic range in format chrom:start-end
--left_sumstats <file>
Summary statistics file
--left_cov <file> Covariance matrix - correlation structure between
variants
--left_covmeta <file>
Covariance matrix SNP info (from LDstore)
--right_sumstats <file>
(Optional) Summary statistics file
--right_cov <file> Covariance matrix - leave blank if same as left_cov
--right_covmeta <file>
Covariance matrix SNP info (from LDstore)
output file arguments:
--outprefix <str> Output prefix
finemapping arguments:
--left_kmax <int> Maximum number of causal variants (default: 5)
--left_kstart <int> Full exploration of sets with #kstart causal variants
(default: 1)
--right_kmax <int> Maximum number of causal variants (default: left_kmax)
--right_kstart <int> Full exploration of sets with #kstart causal variants
(default: left_kstart)
--v_scale <float> Prior variance of the independence prior (default:
0.0025)
--maxiter <int> Max iterations of stochastic search (default: 100000)
--prior <str> Choice of "independence" or "gprior" (default:
independence)
--g <str> g-parameter of the g-prior (default: BRIC). see
Mixtures of g Priors for Bayesian Variable Selection
Liang et al 2008
file parsing arguments:
--sep <str> Column sep (default: tab)
--left_rsidcol <str> RSID column (default: rsid)
--left_chromcol <str>
Chromosome column (default: chrom)
--left_poscol <str> Position column (default: pos)
--left_betacol <str> Beta column (default: beta)
--left_secol <str> Standard error column (default: se)
--left_effalcol <str>
Effect allele column (default: effect_allele)
--left_ncol <str> Sample size column (default: n)
--right_rsidcol <str>
RSID column (default: left_rsidcol)
--right_chromcol <str>
Chromosome column (default: left_chromcol)
--right_poscol <str> Position column (default: left_poscol)
--right_betacol <str>
Beta column (default: left_betacol)
--right_secol <str> Standard error column (default: left_secol)
--right_effalcol <str>
Effect allele columns (default: left_effalcol)
--right_ncol <str> Sample size column (default: n)
{outprefix}.left_configurations.tsv: finemapping results for left dataset
{outprefix}.left_configurations.pkl: pickle of OneDConfigurationSample for left dataset
{outprefix}.right_configurations.tsv: finemapping results for right dataset
{outprefix}.right_configurations.pkl: pickle of OneDConfigurationSample for right dataset
{outprefix}.joint_configurations.tsv: co-localisation results for joint analysis
{outprefix}.joint_configurations.pkl: pickle of TwoDConfigurationSample for joint analysis
{outprefix}.joint_evidence.tsv: Single float giving co-localisation evidence (sum of joint posteriors from {outprefix}.joint_configurations.tsv)