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Imputation performance depends on r2 of nearby SNPs. (a) For common indels, frequency matched SNP imputation performs similar to imputation using all SNPs. (b) For low frequency indels, imputation performance improves rapidly for heterozygous (ref/alt) imputation with > 90% concordance once r2 between indels and SNPs reaches 0.25. However, imputation of alternative homozygous alleles (alt/alt) remains below 15% even when imputed with SNPs in perfect LD.
