Raw SNP files and filtered rQTL files for each family

Following the dDocent pipeline, sequences were trimmed, mapped to the eastern oyster genome, SNPs were called using FreeBayes, and SNPs were filtered (reference the manuscript for details), individual sequences were separated into groups by family. Each family .vcf file was loaded into Onemap independently: FamX_raw.onemap.vcf files above. <br>After linkage map creation and marker ordering in Onemap, markers were thinned for downstream QTL mapping. The ordered, thinned marker files were then converted to Rqtl 4-way cross format for each family: FamX_thinned_bypos_rQTL.csv.

本研究遵循dDocent分析流程，先对序列进行修剪，随后将其比对至美洲牡蛎参考基因组；利用FreeBayes识别单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点，并对SNPs进行过滤（详细流程参见相关手稿）；随后将个体序列按家系划分为不同分组。将每个家系的变异识别格式（Variant Call Format, VCF）文件独立导入至Onemap软件，即上文所述的FamX_raw.onemap.vcf文件。
在Onemap中完成连锁图谱构建与标记排序后，对标记进行稀疏化处理以用于后续的数量性状位点（Quantitative Trait Locus, QTL）定位分析。将经排序与稀疏化处理后的标记文件转换为适配Rqtl的四向杂交群体格式，最终生成各家家系对应的结果文件：FamX_thinned_bypos_rQTL.csv。