Genotypes extraction from GenoEx-GDE, hints for InterGenomics Organisations

This page contains hints on how InterGenomics Organisations may extract genotypes from GenoEx-GDE.

Extract all males raw genotypes (including duplicates) submitted by all InterGenomics Organisations

The following extraction criteria produce a 706 output file which mimics the previously distributed file "file705_$runid_ALL_RAW_DUP.zip":

• Breed = BSW
• Country = SELECT ALL
• Organisation = ANARB, BFRO, CDCB, GENEVAL, LFL, QUALITAS
• Array = SELECT ALL
• Sex = M
• Genotypes extraction = All
• Uploaded between = default interval

Please, note that Interbull Centre (code "IBC") is not selected among the listed Organisations.

Extract all males raw genotypes (avoiding duplicates) submitted by all InterGenomics Organisations

The following extraction criteria produce a 706 output file which mimics the previously distributed file "file705_$runid_ALL_RAW_NODUP.zip":

• 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)
• Uploaded between = default interval

Please, note that Interbull Centre (code "IBC") is not selected among the listed Organisations.

Extract user owned females imputed genotypes uploaded by Interbull Centre as evaluation's result

The following extraction criteria produce a 706 output file which mimics the previously distributed file “country_female_genotypes.txt”:

• Breed = BSW
• Country = SELECT ALL
• Organisation = IBC

• Array = GenoEx InterGenomics 55172

• Sex = F
• Genotypes extraction = All
• Uploaded between = set the dates' interval related to run specific evaluation's results release according to the Interbull Service Calendar

Please note that the in the extracted 706file the field “LABNAME” contains “InterGenomics” and the field “SAMPLEID” contains the runid code (i.e. “2104r” for the April 2021 routine run).

Extract males imputed genotypes uploaded by Interbull Centre as evaluation's result

The following extraction criteria produce a 706 output file which mimics the previously distributed file “file705_ALL_A_IMP_$runid.txt”:

• Breed = BSW
• Country = SELECT ALL
• Organisation = IBC

• Array = GenoEx InterGenomics 55172

• Sex = M
• Genotypes extraction = All
• Uploaded between = set the dates' interval related to run specific evaluation's results release according to the Interbull Service Calendar

Please note that the in the extracted 706file the field “LABNAME” contains “InterGenomics” and the field “SAMPLEID” contains the runid code (i.e. “2104r” for the April 2021 routine run).