Trouble after imputation with minimac
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6.3 years ago
ISB ▴ 30

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!

SNP imputation minimac genetics • 1.7k views
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Entering edit mode
6.3 years ago
venks ▴ 730

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!

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