CDCB file submission protocol for National Evaluation Centers (old)¶

• Table of contents
• CDCB file submission protocol for National Evaluation Centers (old)
  • Important notice
  • Submission content and naming convention
    • Zip filename
    • Zip content

Important notice¶

It is important to note that the files shared with CDCB should NOT contain:

• special characters
• hexadecimal characters
• values in scientific notation.
• characters in foreign alphabet (chinese, japanese, cyrillic, etc)
• letters with accents

Please check your files before submission to identify and correct such issues. Files containing such characters will be immediately rejected.

Submission content and naming convention¶

Zip filename¶

• A single zipped file for each submission should be placed in the NEC's "in" folder of the CDCB sftp.
• NEC staff must create a Redmine ticket to inform CDCB staff of the successful submission. Please contact the CDCB genomics team if your NEC does not have or needs to modify/add your CDCB Readmine access.
• The zip file naming convention is: YYYYMMDDXX_[CDDR/NEC].zip , where
  • YYYYMMDD is the date in 8 bytes, and XX is the batch number (for multiple submissions in a day). E.g. 2020053001
  • NECs participating in the CDDR exchange program submitting CDDR file submissions should use CDDR in the zip file name. E.g. 2020053001_CDDR.zip
  • All NECs, irrespectively of their participation in the CDDR exchange program, should submit any non-CDDR file submissions using NEC in the zip file name. E.g. 2020053001_NEC.zip

Zip content¶

• Every zip file should contain at least 2 files: a pedigree and genotype file.

1. Pedigree file naming convention is: YYYYMMDDXX_pedigree.txt , where YYYYMMDDXX is the same value as in the .zip file. Pedigree file content format is in Interbull's Format200 (EXTERNAL LINK) . If the information is available, TW (twin) or ET (embryo transfer) animals should be identified in position 74-75 instead of the animal status.
   An example record is:
   

   200 HOL840M000000000000 HOLUSAM000000000001 HOLUSAF000000000002 20101228 ET 20130114 ANIMALNAMEHERE                                     USA
   

2. Genotype file naming convention is: YYYYMMDDXX_genotype.csv , where YYYYMMDDXX is the same value as in the .zip file. Genotype file is comma delimited, content is:

   Field order (1)	Num Bytes	Field Format	Ref Note(s)	Field Description
   1	2	CH	4	Evaluation Breed group of animal (alpha code only, no zeros)
   2	19	CH		19 digits Animal Identification in Interbull format: Breed(3)+Country of registration (3)+Sex(1)+ID number (12)
   3	up to 22	CH		sample ID : Identification of the sample when sent to the lab
   4	up to 12	CH	347	Requester ID : AI organization, breed association, or lab requesting the genotyping
   5	1 or 2	CH	348	Laboratory where chip was prepared and scanned. Not Required
   6	1	CH	163	Parentage only indicator: if genotype is for parentage verification only or not only for parentage Not Required
   7	up to 8	CH	349	Group Name - location of animal or organization used to determine CDCB fee Not Required
   8	blank or 1	CH	354	Tissue source that the DNA was extracted from Not Required
   9	up to 12	CH		Chip Barcode: uniquely Identifies the chip which typically contains 24 samples
   10	up to 6	CH		Position of the sample on the chip (row and column)
   11	8	CH		load date : date genotype was added to CDCB database (YYYYMMDD) CDCB Use only
   12	1	CH		Usability Code: usability status of the genotype CDCB Use only
   13	1 or 2	CH	162	Array Number
   14	1 byte per SNP, no commas between SNPs	INT		Genotype string (2) : variable length string of 0,1,2,5 indicating SNP genotypes of BB, AB, AA, --.

NOTES:
⁽¹⁾ For non-required fields, please leave the field blank if data is not available.
⁽²⁾ _Please contact the CDCB genomics team for the SNP order in this format. Please indicate the chip type when request this information

An example record is:

 HO,HOL840M000000000000,003000247244,Acceler,2,,,,4294034076,R03C02,,,1,0112501122202112220201021020221015021025201 [...]