Genotype File Formats

SampleSheet || FinalReport

SampleSheet

CSV, comma delimited, consecutive commas indicate a null column … example values shown in red

[Data …
Sample_ID1 must match FinalReport Sample_ID …
Sample_Plate2
Sample_Name1 must contain animal ID but leading zeros may be excluded (HOUSAF00123456789 = HO
USAF123456789) …
Project* must be organization arranging for genotyping (requester) (Holstein Association USA, ABS, Zoetis, etc.) … 
AMP_Plate2
Well in AMP_Plate2
SentrixBarcode_A1 and SentrixPosition_A1 used for unique genotype identification … 
Sample_Source1 required but may be labeled DNA_source or Tissue_source (hair; blood; semen; tissue, including extracted DNA; nasal) … 
Other columns may be included but are not stored],,,,,,,,,,,,,,,,,,,,,,,,

Sample_ID,Sample_Plate,Sample_Name,Project,AMP_Plate,Well in AMP Plate,SentrixBarcode_A,SentrixPosition_A,Scanner,Date_Scan,Replicate,Parent1,Parent2,Gender,Sample_Source,Study,Subclient,Well on DNA plate,Sex,Family Info,Other_Name,Sire,Dam,Comment

HOITAF12345678903,Master-DLMDNA-2014-1727_1-1,HOITAF12345678903,AIPL,InfWP2014-0380-Reaction1,A01,7996554214,R01C01,,,,,,,Hair,14-177,,B5,Female,,Mona Lisa,HOITAM12345678901,HOITAF12345678902,

HODEUF123456789,Master-DLMDNA-2014-1727_1-1,HODEUF123456789,AIPL,InfWP2014-0380-Reaction1,B01,7996554214,R03C01,,,,,,,Hair,14-177,,C5,Female,,Schoene Maedchen,HOUSAM12345678,HONLDF123456789,

HODEUF123456790,Master-DLMDNA-2014-1727_1-1,HODEUF123456790,AIPL,InfWP2014-0380-Reaction1,C01,7996554214,R05C01,,,,,,,Hair,14-177,,D5,Female,,Tupfen Tulpe,HOUSAM12345679,HONLDF123456790,

1Required; used for processing and storing genotypes.
2Required; stored but only used to investigate problems.

File name:
Year/Month/Day/Sample set within day/Serial number for sample-set submission_Chip type/SampleSheet.zip   2014042812_LDSampleSheet.zip

FinalReport

TXT, tab delimited… example values shown in red

[Header … generated by GenomeStudio]
GSGT Version 1.8.4
Processing Date 04/28/2014 9:17 AM
Content BovineLD_C.bpm
Num SNPs 6909
Total SNPs 6909
Num Samples 262
Total Samples 264
[Data … use “AB” for SNP genotype … 1 column/animal … 1st row is sample ID, and following rows are genotypes with 1 row/SNP]

 

   HOITAF12345678903

   HODEUF123456789

   HODEUF123456790

   HODEUF123456791

   HOITAF12345678904

   …

ARS‑BFGL‑BAC‑10975

   AB

   AB

   AB

   AB

   AB

   …

ARS‑BFGL‑BAC‑11025

   AB

   AA

   AB

   AA

   AB

   …

   ⋮

   ⋮

   ⋮

   ⋮

   ⋮

 

File name:
Year/Month/Day/Sample set within day/Serial number for sample-set submission_Chip type/FinalReport.zip   2014042812_LDFinalReport.zip