Processing DAP Fine-mapping Output

Here, we demonstrate the procedure to convert fine-mapping output from the software SuSiE using an example dataset.

1. Download the sample data set from here

2. Unpack the package in a terminal, using the following command:

tar zxf susie_example.tgz

You should see a gzipped vcf file snp.chr5.vcf.gz and a directory eqtl_susie_out with 1,198 SuSiE fine-mapping output files. Note that each of the fine-mapping file is named as gene_name.dap.out. The processing script will recognize and use the string gene_name.

Each of the SuSiE fine-mapping file is extracted from the SuSiE R object with the following tabular format with no header needed.

Credible_Set SNP PIP

1. Run the utility script susie2enloc to obtain the FastENLOC eQTL input:

susie2enloc -v snp.chr5.vcf.gz -d eqtl_susie_out/ > eqtl.fastenloc.vcf

or obtain a gzipped version:

susie2enloc -v snp.chr5.vcf.gz -d eqtl_susie_out/ | gzip - >  eqtl.fastenloc.vcf.gz