Trouble after imputation with minimac

Question

[ISB]

Hi all,

I have followed Minimac cookbook, http://genome.sph.umich.edu/wiki/Minimac:_1000_Genomes_Imputation_Cookbook#Questions_and_Comments to impute with 1000 genome V3 as reference. However, the output files show alleles as Rs, Is and D`s in stead of A,T,C,G for some of the SNPs. Have anyone experienced this before? Because of this error, I cant convert the files to PED/MAP, or merge them in anyway. So I am basically stuck.

Please let me know if you have any ideas how to handle this.

Thanks!

Answer 1

[venks]

I's and D's just tells you that the data is imputed and on that particular locus it is an Insertion/Deletion. If you don't want this you can remove indels using vcftools --remove-indels. This will get rid of all the multiallelic sites. You then will be able to convert them to plink PED/MAP.

Good luck!