Question: TILLING population GWAS methodology
0
gravatar for rob234king
3.9 years ago by
rob234king580
UK/Harpenden/Rothamsted Research
rob234king580 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 • 1.3k views
ADD COMMENTlink modified 3.9 years ago by vassialk190 • written 3.9 years ago by rob234king580
0
gravatar for vassialk
3.9 years ago by
vassialk190
Belarus
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 3.9 years ago by vassialk190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2001 users visited in the last hour