I'm analyzing some Illumina genotype data and noticing that almost 2% of variants on the array are typed more than once. I consider these measurements to be replicate if they are measuring the same chromosome, position, reference allele, and alternate allele as specified in the PLINK BIM file. It seems that the typical thing people do is remove all but the first replicate in the file using the --list-duplicate-vars option in PLINK. Are there any tools that implement something slightly smarter than this? Like, for example, a desired behavior might be to take a consensus vote amongst the calls from the replicates to decide which one to use. Thanks in advance!