Heterogeneous Stock (HS) Rat Genotypes, Version 4. 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.

本数据集对象中生成数据所使用的全部软件版本已在下方及相关学术论文的方法部分注明：
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

测序数据的解多路复用环节采用fastx_toolkit与fgbio完成；条形码、接头序列及测序质量的修剪步骤由cutadapt与bbDuk执行；利用BWA将测序读段比对至褐家鼠（Rattus norvegicus）参考基因组组装版本mRatBN7.2；通过samtools对测序读段的比对结果完成定量统计；结合从8个HS大鼠创始品系中鉴定得到的共识变异参考面板，使用STITCH完成SNP基因型的填充分析；参考面板中的SNP变异位点通过GATK完成检出；变异位点的筛选过滤借助bcftools实现；全流程质量控制工作由Python完成。