CDCB Whole-Genome parentage certification service¶

• Table of contents
• CDCB Whole-Genome parentage certification service
  • Introduction
  • Policy document and ICAR documentation
  • Operative information
    • Request file
    • Output file
  • Limitations
  • Certificate authorization rules

Introduction¶

This service is provided to US-based nominators, full NAAB members that are also nominators, the NAAB association, and US breed associations.
A requester is entitled to receive an official SNP-based parentage certificate for its own animals, provided the animal is already present in the National Cooperator DatabaseCD.
Effective September 7th, 2026, this service is based on all available SNPs and no longer uses the 195 ISAG PV panel, as recommended by ICAR. The CDCB implementation only considers SNPs that have passed CDCB QC criteria during validation (or subsequent QC updates).
Please note that, since the ICAR-approved methodology differs from the standard parentage verification service normally provided by CDCB, parentage verification results reported in the certificates may differ.

Policy document and ICAR documentation¶

• The policy document for this service is available here
• ICAR guidelines describing the service provided are available here

Operative information¶

Request file¶

• File naming convention: Same as the format 1 naming convention, but with .par as the extension (YYYYMMDD.par*, where * represents your own extension. Example: YYYYMMDD.par_thisismyfile)
• File placement: The input file must be placed in the user CDCB SFTP "in" directory.
• File content: The file content MUST contain 3 fields. Fields MUST be comma-separated, and no header should be included.
• Fields:
1. Animal ID (valid id17)
2. Sire ID (valid id17)
3. Dam ID (valid id17)

• Example:
  

  JE840003000000001,JEUSA000000000002,JE840003000000003
  HO840003000000004,HO840003000000005,HO840003000000006
  

Output file¶

• Output file: The output file will be placed in the "out" folder of the recipient's CDCB SFTP account and will be named as: CDCB_ICAR_parentage_YYYYMMDD_par<ext>_TTTTTT.zip, where:
  • CDCB_ICAR_parentage_ and all blue-colored text are fixed.
  • YYYYMMDD_par<ext> is the input file name provided by the user, with underscores replacing dots in the file name (e.g. YYYYMMDD.par1 = YYYYMMDD_par1)
  • TTTTTT is a unique timestamp used to avoid overwriting the output file in case multiple files with the same name are submitted on the same day.
  • Example: input file called YYYYMMDD.par_thisismyfile. Expected output file will be CDCB_ICAR_parentage_YYYYMMDD_par_thisismyfile_123456.zip

• Content of output file: The content of the zip file will depend on the request.
  • A report file named CDCB_ICAR_parentage_report_YYYYMMDD_par<ext>_TTTTTT.csv (e.g. CDCB_ICAR_parentage_report_YYYYMMDD_par_thisismyfile_123456.csv) will always be provided, regardless of the option selected. This file contains a detailed explanation for each animal included in the input file.
    Fields in this file are:
    • CandidateID: The animal ID provided for the analysis
    • Candidate_SampleID: The sample ID of the genotype for the candidate animal used in the analysis (if the genotype was retrieved from the National Cooperator Database)
    • SireID: The sire ID provided for the analysis
    • Sire_SampleID: The sample ID of the genotype for the sire used in the analysis (if the genotype was retrieved from the National Cooperator Database)
    • DamID: The dam ID provided for the analysis
    • Dam_SampleID: The sample ID of the genotype for the dam used in the analysis (if the genotype was retrieved from the National Cooperator Database)
    • HomozygousSNP_Anim_Sire: Total number of common homozygous SNPs between the candidate animal and its sire.
    • HomozygousSNP_Anim_Dam: Total number of common homozygous SNPs between the candidate animal and its dam.
    • Mend_SIRE_Count: Number of Mendelian conflicts between the animal and sire. An explanation of Mendelian conflicts is available in the CDCB Genomic Dictionary - section Mendelian inheritance conflicts.
    • Mend_SIRE_PCT: Percentage of Mendelian conflicts between the animal and sire, calculated as: (Mend_SIRE_Count / HomozygousSNP_Anim_Sire) * 100
    • Mend_DAM_Count: Number of Mendelian conflicts between the animal and dam. An explanation of Mendelian conflicts is available in the CDCB Genomic Dictionary - section Mendelian inheritance conflicts.
    • Mend_DAM_PCT: Percentage of Mendelian conflicts between the animal and dam, calculated as: (Mend_DAM_Count / HomozygousSNP_Anim_Dam) * 100
    • SIRE_REPORT: Outcome of the analysis. Possible values are: NOT CHECKED, LOW CALL, ACCEPTED, DOUBTFUL, and EXCLUDED. Determination of each category and the thresholds used follow the ICAR guidelines for SNP parentage verification
    • DAM_REPORT: Outcome of the analysis. Possible values are: NOT CHECKED, LOW CALL, ACCEPTED, DOUBTFUL, and EXCLUDED. Determination of each category and the thresholds used follow the ICAR guidelines for SNP parentage verification
      verification":https://www.icar.org/Documents/GenoEx/ICAR%20Guidelines%20for%20Parentage%20Verification%20and%20Parentage%20Discovery%20based%20on%20SNP.pdf
    • COMMENTS: If animals were excluded from the analysis or did not receive a certificate, the reason for the exclusion will be explained in this field. If no errors or issues are found, this field may be empty. Please note that not all comments in this section prevent an animal from receiving a certificate.

• All qualifying animals will receive a separate PDF certificate named Parentage_certificate_<ID_OF_THE_ANIMAL>.pdf (e.g. Parentage_certificate_HOUSA000000000001.pdf).
  • Not all requested animals may qualify for a certificate. The reason will be described in the "COMMENTS" section of the report. In general, except for formal problems in the input file, issues reported for candidate animals will result in no certificate being generated, whereas most issues reported for sire/dam animals will not prevent a certificate from being issued. If the user believes that an error was assigned incorrectly by the system, please submit a Redmine ticket requesting a review.

Limitations¶

• A maximum of 100 certificates per file may be requested. A file containing more than 100 lines will result in rejection of the entire file.
• Duplicate entries within a file are not allowed. If duplicates are present in the input file, the duplicate entries will be excluded from the analysis.
• The content of the certificate cannot be modified and follows the currently available ICAR guidelines. Please note that the certificate requester is embedded in the certificate.

Certificate authorization rules¶

• This service is provided to US-based nominators, full NAAB members that are also nominators, the NAAB association, and US breed associations.
  • Nominators may only request certificates for animals they have nominated, except for AI bulls, which may only be requested by the bull controller stud or by the NAAB association.
  • Nominator rules also apply to full NAAB members that are also nominators. However, these users may also request AI bulls for which they are the bull controller stud.
  • Breed associations may request certificates for any registered animal of the breed they represent (both a valid registration code and at least one animal ID source code "B" are required), and/or for animals they have nominated.
  • The NAAB association may request certificates for any AI male (defined as any participant in the NAAB cross-reference database).