Need inputs - GWAS using VCF file and phenotypic traits

[Sri Kiran Reddy Alla]

Hello everyone,

I am an early research student & first-time user of Tassel. I want to conduct GWAS for seed weights, and I have filtered VCF file in hapmap format, phenotypic traits file in .txt format. 

Experimental design: Augmented design (5 Blocks, n=200 accessions plus 4 checks replicated twice in each block).

My genomic data is not replicated, but my phenotypic data is replicated. Please suggest a recommended model for conducting the analysis and outline the steps to follow for GWAS.

Your help is much appreciated.

Thank you,

Sree.

[Yaman Jabbour]

dear you need first to do Augmented analysis then the results you will get it used to do GWAS analysis

‫في الأربعاء، 11 يونيو 2025 في 8:25 م تمت كتابة ما يلي بواسطة ‪'Sri Kiran Reddy Alla' via TASSEL - Trait Analysis by Association, Evolution and Linkage‬‏ <‪tas...@googlegroups.com‬‏>:‬

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[venkat rami reddy]

Hi Sai Krishna Reddy, 

I see that the experimental design is augmented data. So you need to calculate BLUEs of the genotypes and then perform the GWAS analysis in tassels. Can write me at venkkatr...@gmail.com if you need any specific information or in detail tutorial. 

All the best 

Thanks and Regards,

Yannam Venkat Rami Reddy

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[Muhammad Atif Wahid]

MLM (Q+K) model

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