Toward better understanding of artifacts in variant calling from high-coverage samples

Bioinformatics. 2014 Oct 15;30(20):2843-51. doi: 10.1093/bioinformatics/btu356. Epub 2014 Jun 27.


Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of variant calling methods.

Results: We made 10 single nucleotide polymorphism and INDEL call sets with two read mappers and five variant callers, both on a haploid human genome and a diploid genome at a similar coverage. By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas. We estimated that the error rate of raw genotype calls is as high as 1 in 10-15 kb, but the error rate of post-filtered calls is reduced to 1 in 100-200 kb without significant compromise on the sensitivity.

Availability and implementation: BWA-MEM alignment and raw variant calls are available at scripts and miscellaneous data at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Artifacts*
  • Cell Line
  • Databases, Genetic
  • Genome, Human / genetics
  • Genomics / methods*
  • Genotype
  • Haploidy
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • INDEL Mutation
  • Polymorphism, Single Nucleotide