Question: How to use the imputed Genotype data text file for a gwas study
gravatar for asenathi
20 months ago by
asenathi0 wrote:

Hi all, I'm extremely new to gwas analysis, and I was wondering if someone could help me. I'm currently trying to run a gwas analysis and I was given the following data an imputed genotype text file: This has the animal ID then then 0,1,2 representing the snp's (there is no header) the snps are in order of map text file below Animal ID , 011222200210201020102..... Animal ID , 011222200210201020102..... etc. I was then given a map.txt file with SNP ID ; CHR; BP posistion

I also have a phenotype csv file with Animal ID ; Milk yield(quantitative trait)

I have looked through several websites and softwares and r tools to run an analysis on this data but it none of it is in the input file format they want, I was wondering which file format and which r package would be best to use and how to use it, to run a a gwas analysis. Any Help is appreciated!

Thank you, Aarthie

txt imputed genotype gwas • 617 views
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