Differences between revisions 1 and 3 (spanning 2 versions)
⇤ ← Revision 1 as of 2021-04-20 15:26:55 →
Size: 2545
Editor: SimoneSavoia
Comment:
← Revision 3 as of 2021-04-21 08:20:26 → ⇥
Size: 3162
Editor: SimoneSavoia
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
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). 		{{attachment:GDE_logo_scaled.png}}

== 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.
<<BR>>

=== 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.
<<BR>>

=== 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).
<<BR>>

=== 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).

GDE_logo_scaled.png

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).

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