TILLING population GWAS methodology
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6.7 years ago
rob234king ▴ 610

I have a TILLING population 1500 lines of a plant from EMS induced mutations with height phenotypes. I want to associate snps approx 6000 per line with the phenotype using some kind of GWAS study. I can produce a multi-vcf files of my sample but currently have the snps per sample in one file.

Does anyone know of a tool/package that can do this starting from a vcf file and tab file of line and height measurements?

GWAS • 1.7k views
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Entering edit mode
6.7 years ago
vassialk ▴ 200

There are VCF tools, VCF-miner, NextGene, various variant callers, GATK and R packages, finally you can write your own functions in R and Python. Also you can use traditional stat software like JMP and SPSS/STATA, StatsDirect.

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