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 ?