Please find below some suggestions regarding the genotypes extraction from GenoEx-GDE (for both raw and imputed genotypes):
• To extract from GenoEx-GDE all males raw genotypes (including duplicates) submitted by all InterGenomics organisations (in order to mimic the previously distributed file705_$runid_ALL_RAW_DUP.zip), set the extraction criteria as follow: - Breed = BSW; - Country = SELECT ALL; - Organisation = ANARB, BFRO, CDCB, GENEVAL, LFL, QUALITAS; - Array = SELECT ALL; - Sex = M; - Genotypes extraction = All.
• To extract from GenoEx-GDE all males raw genotypes (avoiding duplicates) submitted by all InterGenomics organisations (in order to mimic the previously distributed file705_$runid_ALL_RAW_NODUP.zip), set the extraction criteria as follow: - Breed = BSW; - Country = SELECT ALL; - Organisation = ANARB, BFRO, CDCB, GENEVAL, LFL, QUALITAS; - Array = SELECT ALL; - Sex = M; - Genotypes extraction = Best only (the option “Best only” identifies the genotype with highest call rate among the available ones for an animal ID, regardless uploading organisation or chip array density - among the genotypes the user has access to thanks to sharing permissions).
• To extract from GenoEx-GDE females imputed genotypes (in order to mimic the previously distributed “$CTR_female_genotypes.txt”), set the extraction criteria as follow: - Breed = BSW; - Country = SELECT ALL; - Organisation = IBC; - Array = GenoEx InterGenomics 55172; - Sex = F; - Genotypes extraction = All. Please note that the in the extracted 706file the field “LABNAME” will contain “InterGenomics” and the field “SAMPLEID” will contain the runid code (“2104r” for the April 2021 routine run).
• To extract from GenoEx-GDE males imputed genotypes (in order to mimic the previously distributed “file705_ALL_A_IMP_$runid.txt”), set the extraction criteria as follow: - Breed = BSW; - Country = SELECT ALL; - Organisation = IBC; - Array = GenoEx InterGenomics 55172; - Sex = M; - Genotypes extraction = All. Please note that the in the extracted 706file the field “LABNAME” will contain “InterGenomics” and the field “SAMPLEID” the runid code (“2104r” for the April 2021 routine run).