SQLite database of variants in Collaborative Cross founder mouse strains

A SQLite database with two tables: "description" and "variants". The description table includes URLs for the source files. The "variants" table contains the data, including the fields snp_id, chr (1-19, X, Y, MT), pos (in basepairs, GRCm38/mm10 build), alleles (major and minor alleles), sdp (strain distribution pattern, used by R/qtl2), ensembl_gene, consequence, the 8 founders' genotypes (as numeric codes with 1 = major allele), and type (snp/indel/SV). The ensembl_gene field may contain multiple comma-separated values. The consequence field may also contain multiple comma-separated values, and each has the form "gene:consequence".

The script used to create it is at GitHub.