La Jolla Institute for Immunology, La Jolla, CA 92037, USA
Implements a wrapper for the FINEMAP package (http://www.christianbenner.com/), to generate the fine mapped variants corresponding to an input GWAS or eQTL summary statistics
Prerequisites
Download the 1000G Genotype data (we've used hg19 as the reference genome).
Follow the tutorial: https://cran.r-project.org/web/packages/snpsettest/vignettes/reference_1000Genomes.html.
The path containing this 1000G genotype data needs to be provided as a configuration parameter (check the parameter *GENOTYPEDIR* in the configuration files, described below).
Install these R libraries: data.table, dplyr, GenomicRanges, gridExtra
Download the package LDSTORE2 (binary executable) from http://www.christianbenner.com/.
The path of this executable needs to be provided as a configuration parameter (check the parameter *ldstoreexec* in the configuration files, described below)
Download the package FINEMAP (binary executable) from http://www.christianbenner.com/.
The path of this executable needs to be provided as a configuration parameter (check the parameter *finemapexec* in the configuration files, described below)
Fine-mapping of eQTL summary statistics
First edit the configuration file configfile_eQTL.yaml.
A sample eQTL smmary statistics is provided in the file Data/Example_eQTL_data.txt for the users.
User needs to edit the configuration file according to the file / directory paths, contents of the summary statistics file.
.. Note ..
1. In the configuration file, user needs to provide at least one of *betaCol* (column containing the beta statistics) or *ORCol* (column containing the odds ratio).
2. Either user needs to provide the *SampleSizeCol* (column containing the sample size information) or put the integer value in the field *TotalSample* (total number of samples / donors used in the eQTL study).
3. The parameter *geneIDCol* (column containing the gene ID, preferably in Ensemble ID format) is mandatory.
Once the configuration file is edited, user can use the script finemap_script.sh to execute the fine-mapping.
Fine-mapping of GWAS summary statistics
First edit the configuration file configfile_GWAS.yaml.
A sample GWAS smmary statistics is provided in the file Data/Example_GWAS_data.txt for the users.
User needs to edit the configuration file according to the file / directory paths, contents of the summary statistics file.
.. Note ..
1. In the configuration file, user needs to provide at least one of *betaCol* (column containing the beta statistics) or *ORCol* (column containing the odds ratio).
2. Either user needs to provide the *SampleSizeCol* (column containing the sample size information) or put the integer value in the field *TotalSample* (total number of samples / donors used in the eQTL study).
3. The parameters *chrCol* (column containing the chromosome) and *posCol* (column containing the SNP position) are mandatory.
4. User should provide the parameter *AFCol* (column containing the allele frequency information), if available.
5. The *OFFSET* parameter specifies the window surrounding a lead GWAS SNP used to define a GWAS locus.
Once the configuration file is edited, user can use the script finemap_script.sh to execute the fine-mapping.
Output
With respect to the specified output directory (parameter OutDir in either of these configuration files), check the folders cond (output of stepwise conditioning) and sss (output of shotgun stochastic search).
1. *FINAL_summary_credible_set.txt* : File containing the GWAS loci, credible causal sets and the corresponding SNPs.
2. *FINAL_top_snp_credible_set.txt* : All the SNPs listed in the credible causal sets.
Contact
For any queries, please create an issue and we’ll respond. Otherwise, please e-mail
Fine mapping of GWAS and eQTL summary statistics
Sourya Bhattacharyya
La Jolla Institute for Immunology, La Jolla, CA 92037, USA
Implements a wrapper for the FINEMAP package (http://www.christianbenner.com/), to generate the fine mapped variants corresponding to an input GWAS or eQTL summary statistics
Prerequisites
Fine-mapping of eQTL summary statistics
First edit the configuration file configfile_eQTL.yaml.
A sample eQTL smmary statistics is provided in the file Data/Example_eQTL_data.txt for the users.
User needs to edit the configuration file according to the file / directory paths, contents of the summary statistics file.
Once the configuration file is edited, user can use the script finemap_script.sh to execute the fine-mapping.
Fine-mapping of GWAS summary statistics
First edit the configuration file configfile_GWAS.yaml.
A sample GWAS smmary statistics is provided in the file Data/Example_GWAS_data.txt for the users.
User needs to edit the configuration file according to the file / directory paths, contents of the summary statistics file.
Once the configuration file is edited, user can use the script finemap_script.sh to execute the fine-mapping.
Output
With respect to the specified output directory (parameter OutDir in either of these configuration files), check the folders cond (output of stepwise conditioning) and sss (output of shotgun stochastic search).
Contact
For any queries, please create an issue and we’ll respond. Otherwise, please e-mail
Sourya Bhattacharyya: sourya@lji.org
Ferhat Ay: ferhatay@lji.org