ReviewBioinformatics (Oxford, England)2014
Toward better understanding of artifacts in variant calling from high-coverage samples.
Review in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 548 papers.
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Who cites it
548 citing papers in PubMed.
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- Benchmarking genomic variant calling tools in inbred mouse strains: recommendations and considerations.Genetics · 2026Article
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- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- GapSense: Similarity Estimation-Based Gap Filler with TGS-Reads for Genome Assemblies.Interdisciplinary sciences, computational life sciences · 2026Article
- Exome-wide association study of blood lipids in 1,158,017 individuals from diverse populations.Nature genetics · 2026Article
- Mitogenome characteristics of two Tetragonula stingless bees (Hymenoptera: Apidae) from Hainan, China.Journal of insect science (Online) · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Epigenetic Inhibitor 5-Azacytidine Triggers DIM-2/DIM-5-Dependent Mutagenesis in H3K9me3-Enriched Regions ofJournal of fungi (Basel, Switzerland) · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
488 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
motivationWhole-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.
resultsWe 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 http://bit.ly/1g8XqRt scripts and miscellaneous data at https://github.com/lh3/varcmp. CONTACT: hengli@broadinstitute.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.