Heterogeneous Stock (HS) Rat Genotypes, Version 5. In Genotype data from: NIDA Center for GWAS in Outbred rats

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.