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This Venn diagram displays how markers in the reference panels for each imputation program and the original 1000 Genomes data overlap on chromosome 20. Unique lists of genomic position were compared across datasets.
The original dataset and the MaCH reference panels came with genomic position in the format of VCF files. For the BEAGLE reference panel, genomic position was determined with the .markers files and with the legend file for IMPUTE2.