I want to performed GWAS. My data are SNP markers. How the SNP data file in Numeric format can be converted to Hapmap format?
Hi, Khalil Zaynali Nezhad!
I think I can give you tips to help you to perform this conversion, but I will need to understand better your data format.
Is "numeric format":
* the [0, 1, 2 (copies of alternative allele)] format?
* the [1, 2, 3, 4 (ATGC)] VCF/hierfstat format?
* the [1 1, 1 2, 2 2] PED file format?
Depending on the numeric format, you can load it directly using Tassel and Export it to HapMap using Tassel as well.
In summary, Tassel can handle a lot of "SNP data" format, and it is possible for you to convert your file to HapMap using this tool.
If possible, you can attach a "Print Screen" showing a small portion of your data, and we can give you better directions for performing the conversion.
I hope this answer helps you.
Best,
João
Dear Dr. João Paulo Gomes Viana
Hello
Many thanks for your suggestion.
I will send a print screen soon.
That will be kind of you if you send your email address
my email is [email protected]
All the best
Khalil Zaynali Nezhad
Dear Dr. João Paulo Gomes Viana Hello Many thanks for your suggestion. Attached you can find a print screen of my data file in TASSEL. I look forward hearing from you. My email is [email protected] All the best Khalil Zaynali Nezhad
Hi, Khalil Zaynali Nezhad !
Sorry for the late reply.
I've sent you an e-mail with some hints about the HapMap conversion based on that Print Screen.
Cheers,
João
Hi Mr. João Paulo Gomes Viana
I have struggled with the same problem. I wish you had shared your solution under this title because I wanted really figure out this annoying problem. I couldn't find describing solution anywhere. So if my request doesn't bother you, could you send me your solution under this title?
Thanks in advance
Best
Uğur
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