The indel imputation results in Figure 2d show some differences to the SNP imputation results at high frequencies, but are otherwise broadly similar. We investigated this issue and discovered that indels within 50bp of another indel had noticeable lower imputation accuracy than more isolated indels. Figure 3 shows the imputation performance of indels stratified by distance to another indel, together with the SNP imputation results. This figure shows that isolated indels can be imputed with very similar levels of accuracy to SNPs.
