To illustrate the utility of ANNOVAR in identifying causal genes for Mendelian diseases with recessive inheritance, we synthesized a whole-genome data set with ∼4.2 million SNVs and ∼0.5 million indels. These variants include all variants generated by Illumina on a male Yoruba subject (ftp://ftp.sanger.ac.uk/pub/rd/NA18507/) (14), as well as two known causal mutations for Miller syndrome (G->A mutation at chr16: 70608443 and G->C mutation at chr16: 70612611, representing G152R and G202A in the DHODH gene). We tested the variants reduction procedure on this data set using ANNOVAR, to examine whether we can identify a small subset of candidate genes that include the causal gene DHODH.
