An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

Data inputs for the manuscript "An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster Crassostrea gigas". Includes:

Data from Sutherland et al. 2020, not originally uploaded and uploaded with permission from primary author:

- populations_single_snp_HWE.raw (plink format, single-SNP per locus filtered output from Stacks populations module)

- populations.snps.vcf (as above, but VCF format)

New data, multilocus genotypes from the pilot study from the present analysis:

- R_2022_08_04_S5XL.xls (initial run samples using Cgig_v.1.0 amplicon panel)

- R_2022_10_07_S5XL.xls (second run using Cgig_v.1.0 amplicon panel)

- my_data_ind-to-pop_annot (tab-delim text file interp of populations; note: samples 1601-1608 are cultured samples from China, not wild samples, and this is dealt with in the analysis script)

- selected_mnames.csv (tab-delim text file that outlines each marker name and the reason it was included in the design)

- GBMF_pilot_sample_ID_barcode_run_from_variantCaller_output_2023-07-27.xlsx (Excel file showing run name, barcode ID, and sample ID for the pilot study)

- rubias_142_ind_364_loc_2024-04-03.txt (rubias file, all filtered loci for parentage analysis)

- rubias_142_ind_328_loc_2024-04-03.txt (rubias file, all filtered loci, and any loci with significant Mendelian incompatibilities removed, please see published article)

New data, multilocus genotypes from the Oregon State University (OSU) Molluscan Broodstock Program (MBP):

- R_2023_07_26_12_44_23_user_GSS5PR-0268-78-Ampseq_Oyster_20230725.xls (OSU CHR8 samples using Cgig_v.1.0 amplicon panel)

- my_data_ind-to-pop_annot_OSU_MBP.txt (population map, will need to rename as my_data_ind-to-pop_annot.txt to match requirement in scripts).