Precomputed Eigen scores are stored in tab-delimited files. Scores have been calculated for each possible SNV in the hg19 human reference genome. These are compressed with the bgzip utility, and indexed with tabix, both of which are part of the Samtools software suite. In addition, tabix provides a means of efficiently extracting subsets of the data defined by genomic regions. For example, from the command line
"tabix Eigen_hg19_noncoding_annot_chr1.tab.bgz 1:20000-30000 > Subset.txt"
extracts all variants on chromosome 1 from position 20,000 through 30,000 and writes them to the file Subset.txt. In this example, the tabix index file, Eigen_hg19_noncoding_annot_chr1.tab.bgz.tbi, needs to be in the same directory as the main data file Eigen_hg19_noncoding_annot_chr1.tab.bgz. Samtools, including bgzip and tabix, is available at http://samtools.sourceforge.net. A perl script for scoring multiple variants at once can be found here.
The precomputed Eigen and Eigen-PC v1.1 scores can be downloaded here. A previous version of the scores (v1.0) is available here (In v1.1 we added some missing positions in the v1.0 version). For downloading the files we recommend using the wget utility; e.g. `wget -c https://xioniti01.u.hpc.mssm.edu/v1.1/Eigen_hg19_noncoding_annot_chr1.tab.bgz'.
The training and testing datasets used in the Eigen paper are available for download here.