Diff for "public/GDE_download_data_IGorgs"

Differences between revisions 2 and 5 (spanning 3 versions)

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

public/GDE_download_data_IGorgs (last edited 2021-04-21 08:22:52 by SimoneSavoia)

-  ⇤ ← Revision 2 as of 2021-04-21 07:41:29 → 
  Size: 2770
  Editor: SimoneSavoia
  Comment:
+   ← Revision 5 as of 2021-04-21 08:22:33 → ⇥
  Size: 3123
  Editor: SimoneSavoia
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 5:
-This page contains hints on how InterGenomics Organisations may extract genotypes from GenoEx-GDE.
+This page contains hints on how !InterGenomics Organisations may extract genotypes from !GenoEx-GDE.
 Line 10:
- * Breed = BSW; 
 * Country = SELECT ALL; 
 * Organisation = ANARB, BFRO, CDCB, GENEVAL, LFL, QUALITAS; 
 * Array = SELECT ALL; 
 * Sex = M; 
 * Genotypes extraction = All.
+ * Breed = BSW 
 * Country = SELECT ALL 
 * Organisation = ANARB, BFRO, CDCB, GENEVAL, LFL, QUALITAS
 * Array = SELECT ALL
 * Sex = M
 * Genotypes extraction = All
 * Uploaded between = default interval
-Line 18:
+Line 19:
+<<BR>>
-Line 23:
+Line 24:
- * 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).
+ * 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
-Line 31:
+Line 33:
+<<BR>>
-Line 35:
+Line 38:
- * Breed = BSW; 
 * Country = SELECT ALL; 
 * Organisation = IBC; 
 * Array = GenoEx InterGenomics 55172; 
 * Sex = F; 
 * Genotypes extraction = All.
+ * 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
-Line 42:
+Line 46:
-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).
+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). 
<<BR>>
-Line 47:
+Line 52:
- * 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” contains “InterGenomics” and the field “SAMPLEID” contains the runid code (i.e. “2104r” for the April 2021 routine run).
+ * 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).