Pedigree-based genome-wide imputation using a low-density amplicon panel for the highly polymorphic Pacific oyster Crassostrea (Magallana) gigas

Files to support the analysis of the Pacific oyster panel imputation project.all_inds_wgrs_and_panel_biallele_only_fi3_imputed.vcf.gz = post-FImpute3 imputation VCF filefi3_loci_by_inds_all_imputed_chr.txt = post-FImpute3 imputation text file (in AlphaImpute2 format)mpileup_calls_noindel5_miss0.15_SNP_q99_avgDP10_biallele_minDP10_maxDP10000_minGQ20_miss0.15_MAF0.05_offspring_only_rename.bcf = offspring (renamed samples) empirical genotypes by panel BCF fileG0923-21-VIUN_SampleInventory_V2_recd_2024-08-16.txt = offspring phenotype fileoffspring_ld_samplelist_for_rename.txt = correspondence between IonCode and sample for offspring amplicon panel dataparent_ld_samplelist.txt = correspondence between IonCode and sample for parent amplicon panel dataG0923-21-VIUN_IonCode-to-SampleID_Key.xlsx = source IonCode to sample ID from service providermpileup_calls_noindel5_miss0.1_SNP_q99_avgDP10_biallele_minDP5_maxDP100_minGQ20_miss0.1_MAF0.05.bcf = parent and offspring wgrs genotypes (n = 424,951 variants, 186 indivs)mpileup_calls_noindel5_miss0.15_SNP_q99_avgDP10_biallele_minDP10_maxDP10000_minGQ20_miss0.15_MAF0.05.bcf = parent and offspring amplicon panel genotypes (n = 1,257 variants, 248 indivs; note: original IonCode identifiers)