Question: TILLING population GWAS methodology
gravatar for rob234king
3.2 years ago by
UK/Harpenden/Rothamsted Research
rob234king560 wrote:

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 • 1.1k views
ADD COMMENTlink modified 3.2 years ago by vassialk190 • written 3.2 years ago by rob234king560
gravatar for vassialk
3.2 years ago by
vassialk190 wrote:

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.

ADD COMMENTlink written 3.2 years ago by vassialk190
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