Processing DAP Fine-mapping Output

Here, we demonstrate the procedure to convert fine-mapping output from the software package DAP 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 dap_example.tgz

You should see a gzipped vcf file snp.chr5.vcf.gz and a directory eqtl_dap_out with 1,198 DAP 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. The files are direct output from DAP, no additional edit/processing is needed.

1. Run the utility script dap2enloc to obtain the FastENLOC eQTL input:

dap2enloc -v snp.chr5.vcf.gz -d eqtl_dap_out/ > eqtl.fastenloc.vcf

or obtain a gzipped version:

dap2enloc -v snp.chr5.vcf.gz -d eqtl_dap_out/ | gzip - >  eqtl.fastenloc.vcf.gz