Data in this release contains genotypes for 6,147 N/NIH heterogeneous stock (HS) outbred rats from the breeding colony MCW: NMcwi:HS #2314009, RRID:RGD_2314009. 

Description of contents:
round8_genotypes_PLINK.zip
This zipped file contains the PLINK binary files:
round8_unpruned.bed
round8_unpruned.bim
round8_unpruned.fam

Oxford text genotype data
round8_unpruned.gen
round8_unpruned.sample

--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.

--Oxford text genotype file format: A text file with no header line, and one line per variant with 3N+5 fields where N is the number of samples. Each line stores information for a single SNP. The first five fields are:
Chromosome code
SNP ID
Base-pair coordinate
Allele 1 (usually minor)
Allele 2 (usually major)
Each subsequent triplet of values then indicate likelihoods of homozygote A1, heterozygote, and homozygote A2 genotypes at this SNP, respectively, for one sample. If they add up to less than one, the remainder is a no-call probability weight.



Technical details:
Rat Genome assembly: Rnor_6.0

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 v1.9.1
• bwa-0.7.12
• picard-tools-1.141
• GATK IndelRealginer v3.5 
• Beagle v4.1
• impute-2.3.2
• java openjdk version “1.8.0_191” 
• python 2


Demultiplexing was performed using fastx_toolkit. Barcode, adapter and quality trimming was performed using Cutadapt. The Rattus norvegicus genome assembly rn6 was used as the reference genome for read alignment with the BWA software.  We then used GATK IndelRealginer to improve alignment quality by locally realigning reads around a reference set of known indels in 42 whole-genome sequenced inbred rat strains, including the eight HS progenitor strains. Variants were called, and genotype likelihoods were computed at variant sites using ANGSD, under the SAMtools model for genotype likelihoods (ANGSD-SAMtools). Beagle was used to improve the genotyping within the samples without the use of an external reference panel. We used a combination of existing sequencing and array genotyping data from the HS rat founder and other inbred laboratory rat strains (Hermsen et al. 2015) as reference panel for imputation. Imputation by IMPUTE2 was performed in 5Mb windows using the aforementioned reference panels and genetic maps.