Quantitative trait Association analysis of Animal genetic data

Question

[deepue]

Hello,

I have phenotype(pheno.txt) and genotype (data.map, data.ped) data of Shoebill. I would like to see if any marker is associated with the phenotype beak length. Also, to identify how much phenotype variance is being explained by the top markers. I have issues in using PLINK as it is not allowing the chromosomes numbers greater than 24. How to achieve this? Is there any other program which can help in doing?

Thanks

[akang]

You have to use --autosome-num flag followed by the chromosome number. Example --autosome-num 32