All software versions used to generate the data in this object are noted below and in the Methods section of the associated publication: fastx_toolkit 0.0.14 cutadapt 4.1 fgbio 1.3.0 bbDuk 38.94 BWA 0.7.17 samtools 1.14 picard 2.25.7 STITCH 1.6.6 GATK 4.2.0 bcftools 1.14 PLINK 1.9 Python 3.10 Demultiplexing was performed using fastx_toolkit and fgbio. Barcode, adapter, and quality trimming was performed using cutadapt and bbDuk. Reads were aligned to the Rattus norvegicus genome assembly mRatBN7.2 using BWA. Read mapping was quantified using samtools. SNP genotypes were imputed using STITCH and a reference panel of consensus variants identified from eight HS rat founder strains. Reference panel SNPs were called using GATK. Variants were filtered using bcftools. Quality control was conducted using Python.

This collection contains genotype data collected as part of the NIDA Center for GWAS in Outbred rats and more than 10 additional research projects that use N/NIH heterogeneous stock (HS) outbred rats. We obtain genotypes for DNA samples derived from rats that are phenotyped by different research projects. We use these genotypes to perform genome wide association studies (GWAS) and a number of related analyses. Data in this release contains genotypes for 14,505 N/NIH heterogeneous stock (HS) outbred rats from the breeding colonies MCW: NMcwi:HS RRID:RGD_2314009, and WFU: NMcwiWFsm:HS RRID:RGD_13673907, the University of California San Diego: RRID: RGD_155269102, the University of Tennessee Health Sciences Center, or Oregon Health and Sciences University.