Data in this release contains genotypes for 17,812  N/NIH heterogeneous stock (HS) outbred rats from the breeding colonies MCW: NMcwi:HS #2314009, RRID:RGD_2314009, WFU: NMcwiWFsm:HS #13673907, RRID:RGD_13673907, and HS West: McwiWfsmAap:HS #155269102, RID:RGD_155269102. 

Description of contents:
PLINK binary format
--round10_2.bed
--round10_2.bim
--round10_2.fam
Variant Call Format
--round10_2.vcf.gz
--round10_2.vcf.gz.tbi
Genotype Log and Quality Report
--round10_2_genotyping_log.csv
--round10_2_report.html

–-Variant Call Format (VCF): specifies the format of a text file for storing gene sequence variations. A header begins the file and provides metadata describing the body of the file. The body is tab separated into 8 mandatory columns and an unlimited number of optional columns for other information on the samples.
--PLINK binary format: .bed is the PLINK binary biallelic genotype table. This is the primary representation of genotype calls at biallelic variants. The .bed file is accompanied by .bim (Variant information) and .fam (Sample information) files.
--Genotyping Log and Report: includes list of individuals that have passed quality control. Report is a summary of the genotyping results. 

Technical details:
--Rat Genome assembly: mRatBN7.2 (NCBI: GCF_015227675.2) 

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.

To obtain the best possible HS founder imputation reference panel, we used consensus bi-allelic homozygous SNP calls from three different HS rats founder datasets. The first dataset was produced from publicly available 30.34x coverage WGS sequences (NCBI: PRJNA487943) using the Genome Analysis Toolkit (GATK) joint calling workflow. In this dataset, BN/SsN and MR/N are female, and other rats are male. The second dataset was produced using the same GATK joint calling workflow on 41.81x coverage WGS sequences. In this dataset, all eight HS founders are male. The third dataset was produced on the same 41.81x coverage WGS sequences, but using the DeepVariant multi-sample calling workflow. For autosomal chromosomes and chromosome X, 7,406,667 and 184,934 SNPs that had the concordant homozygous genotypes for each founder across all three callsets were retained respectively. Because the BN/SsN and MR/N in the first dataset are female, we dropped them from the concordance check process for chromosome Y and mitochondria, resulting in 5,220 concordant homozygous SNPs for chromosome Y and 117 for mitochondria. In total, 7,596,938 SNPs were retained for the reference panel.