Fig. 3.

Analysis of variant calling errors in HiQ datasets. A detailed characterization of errors in variants identified by the TVC using the optimize parameters provided by the manufacturer. a Fraction of true-positive (red) and false-positive (black) variants occurring with more than 2 or more than 3 alternate alleles in the corresponding VCF file. b Fraction of false-negative SNP (blue) and indels (green) with read depth <10 in the corresponding sample. The indel length of false positive (red), true positive (green) and false negative (blue) calls identified across the nine HiQ datasets is analyzed in c. True positive calls are highly consistent across the nine HiQ samples, while false-positive calls are often run specific as suggested by the density plot (d), that evidences the recurrence of false positives (red) and true positives (green)