VNTR genotyping using PacBio data. (A) RU count estimation on simulated PacBio reads as a function of RU count and coverage for three medically relevant VNTRs: INS (RU length 14 bp), CSTB (12 bp), and HIC1 (70 bp). adVNTR performance is compared to a naïve method. (B) The effect of RU length on count accuracy over 2944 VNTRs (30418 tests). (C) Mendelian consistency of genotypes at four VNTR loci in the Chinese Han and Ashkenazi trios. Note that MAOA results are consistent with its location on Chr X. (D) LR-PCR–based validation of genotypes at five disease-linked VNTRs in NA12878. Red arrows correspond to VNTR lengths estimated by multiplying predicted RU counts with RU lengths. (E) Fraction of consistent calls and number of calls across 2944 VNTRs in Ashkenazi Jew (AJ) and Chinese trios from GIAB and NCBI SRA. (F) Fraction of consistent calls allowing for off-by-one errors.
