Converting Excel Genotype data to Vcf or Hapmap

[Akani Hlungwana]

Dear TASSEL Community,
I hope you are all well,
I currently have a genotype SNP dataset in Excel format, as shown in the attached picture. I would like to kindly ask for guidance on how to convert the dataset into either VCF or HapMap format for downstream analysis in TASSEL and GWAS studies.

Any guidance, examples, or recommended scripts/software would be greatly appreciated.
Thank you very much for your assistance and support.

[Terry Casstevens]

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load

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[Akani Hlungwana]

Hello,

I did go through the user manual and saved the Excel document as Text (Tab delimited). However, when I tried to load it on TASSEL, it gave an error. Please see the attached picture for reference.

[Hugo Cuevas]

How many SNP and samples do you have?

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[Akani Hlungwana]

the dataset consists of 9,065 SNP markers genotyped across 336 samples. 

[Terry Casstevens]

If you format it as Hapmap, the file extension should be .hmp.txt

If you format it as VCF, the file extension should be .vcf

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[Hugo Cuevas]

Since it is a small data set you can prepare the hapmafile in Excel, then copy/paste to save the file as name.hmp.txt.

1 - transpose the data file to get row of SNP.

2 - add the colums and name of the hapmap format.

3 - copy/paste to save as name.hmp.txt

4- open in Tassel 

Remember chromosome a bp positon must be in an acending order.

Best,

Hugo

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[Chandika RG]

Hello Akani,

I would manually convert the sheet to match the HapMap format. 

Copy all data and transpose paste in a new Excel sheet. Check the column name of the from - 
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load
Insert all required additional columns and set them to NA for each entry. 

Save the transformed data with extension .hmp.txt - it is a tab-delimited file. 

Best,
Chandika

[Akani Hlungwana]

Hello everyone,  
Thank you all for your support — it worked successfully.

[Muhammad Atif Wahid]

consult maizwgenetics

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