Project

General

Profile

New SNP Chip Validation Process Requirements

 

The above data is to be submitted to CDCB in 3 files

1) Description of the SNP (SNP manifest/map file):

Name,Index,Chr,Position
SNP_Name_1,1,19,123456789
SNP_Name_2,2,30,11223344
SNP_Name_3,3,5,98765432
SNP_Name_4,4,1,123400000
  • The above columns are REQUIRED, with the preferred order as shown

2) Genotypes (Final Report file):

[Header]
Version    1.1.1
Processing Date 14-Mar-2023 03:44:44 PM
Content Test
Num SNPs        4
Total SNPs      4
Num Samples     3
Total Samples   3
[Data]
        AB01234567        AB01234568        AB01234569
SNP_Name_1        BB        AA        AB
SNP_Name_2        AB        AB        AB
SNP_Name_3        AA        AB        AA
SNP_Name_4        BB        BB        BB
  • Matrix format is preferred (rows are SNP, columns are samples)
    • Standard format (all data in rows) can be submitted if matrix format is not available
  • Sample_ID in the genotype file should match the Sample_ID in the sample sheet file

3) Information about the submitted samples (Sample sheet file):

[Header],,,,,,,,,,,,,,,,,,,,,,,
Investigator Name,"Doe, John",,,,,,,,,,,,,,,,,,,,,,
Project Name,2023031411_ABC_AB,,,,,,,,,,,,,,,,,,,,,,
Experiment Name,,,,,,,,,,,,,,,,,,,,,,,
Date,44916,,,,,,,,,,,,,,,,,,,,,,
[Manifests],,,,,,,,,,,,,,,,,,,,,,,
A,A_Dairy_Chip,,,,,,,,,,,,,,,,,,,,,,
[Data],,,,,,,,,,,,,,,,,,,,,,,
Sample_ID,Sample_Plate,Sample_Name,Project,AMP_Plate,Sample_Well,SentrixBarcode_A,SentrixPosition_A,Scanner,Date_Scan,Replicate,Parent1,Parent2,Gender,Sample Type
AB01234567,123456,HOUSA000000000001,Project1,222222,E1,200000000000,R01C01,,,,,,,Tissue
AB01234568,123456,HOUSA000000000002,Project1,222222,B2,200000000001,R01C02,,,,,,,Tissue
AB01234569,123456,HOUSA000000000003,Project1,222222,C3,200000000002,R01C03,,,,,,,Tissue
  • At minimum, the Sample sheet file must contain columns for Sample_ID, Sample_Name, Barcode, and Position

For additional details on the file formats, please see:
https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/CDCB_Accepted_genotype_file_formats

 

Redmine Appliance - Powered by TurnKey Linux