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.