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. 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（dDocent pipeline）对序列进行修剪，并将其比对至东部牡蛎基因组；随后采用FreeBayes软件调用单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs），并对所得SNPs进行过滤（详细方法参见手稿）。按家系对个体序列进行分组，将每个家系的VCF（Variant Call Format，VCF）文件独立导入至Onemap软件，对应文件为前述FamX_raw.onemap.vcf系列文件。在Onemap软件中完成连锁图谱构建与标记排序后，为后续的数量性状基因座（Quantitative Trait Locus，QTL）定位工作，对标记进行稀疏化处理。最后，将每个家系经排序与稀疏化后的标记文件转换为Rqtl软件包的四向杂交群体格式，对应输出文件为FamX_thinned_bypos_rQTL.csv。