DNA sequencing and variant discovery in the BXD family of mice

Whole-genome DNA sequencing data was generated from members of the BXD family of recombinant inbred mice, as well as from the C57BL/6J and DBA/2J parental strains. F2 crosses and advanced intercrosses of female C57BL/6J and male DBA/2J inbred mice have been inbred for many generations, producing RILs that are unique mosaics of C57BL/6J and DBA/2J haplotypes. Spleens from each mouse were whole-genome sequenced using the 10X Genomics Chromium platform. FASTQ files were aligned to the mm10/GRCm38 reference genome, and VCF files were generated using the Genome Analysis ToolKit (GATK).