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Keyword

variant calling

Description: Variant calling is a bioinformatics process that identifies genetic differences, such as single-nucleotide variants and insertions or deletions, from sequencing data.
OpenAlex ID: keywords/variant-calling
The Sequence Alignment/Map format and SAMtools
2009 · Heng Li, Bob Handsaker, et al. · Bioinformatics · 61,856
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Fast and accurate short read alignment with Burrows–Wheeler transform
2009 · Heng Li, Richard Durbin · Bioinformatics · 58,449
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Twelve years of SAMtools and BCFtools
2021 · Petr Danecek, James K Bonfield, et al. · GigaScience · 15,464
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
2014 · Bruce J. Walker, Thomas Abeel, et al. · PLoS ONE · 9,212
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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
2013 · Geraldine A. Van der Auwera, Mauricio O. Carneiro, et al. · Current Protocols in Bioinformatics · 6,675
Mapping short DNA sequencing reads and calling variants using mapping quality scores
2008 · Heng Li, Jue Ruan, et al. · Genome Research · 2,639
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A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
2012 · Michael Quail, Miriam E Smith, et al. · BMC Genomics · 2,029
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Scaling accurate genetic variant discovery to tens of thousands of samples
2017 · Ryan Poplin, Valentin Ruano-Rubio, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1,931
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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
2019 · Aaron M. Wenger, Paul Peluso, et al. · Nature Biotechnology · 1,829
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A universal SNP and small-indel variant caller using deep neural networks
2018 · Ryan Poplin, Pi-Chuan Chang, et al. · Nature Biotechnology · 1,814
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The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
2014 · Todd J Treangen, Brian D Ondov, et al. · Genome biology · 1,656
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Strelka2: fast and accurate calling of germline and somatic variants
2018 · Sangtae Kim, Konrad Scheffler, et al. · Nature Methods · 1,638
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Harnessing the power of RADseq for ecological and evolutionary genomics
2016 · Kimberly R. Andrews, Jeffrey M. Good, et al. · Nature Reviews Genetics · 1,490
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LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
2012 · Andreas Wilm, Pauline Poh Kim Aw, et al. · Nucleic Acids Research · 1,372
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VarScan: variant detection in massively parallel sequencing of individual and pooled samples
2009 · Daniel C. Koboldt, Ken Chen, et al. · Bioinformatics · 1,348
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
2011 · Tim Carver, Simon R. Harris, et al. · Bioinformatics · 1,217
Comparison of Sequencing Utility Programs
2013 · Erik Aronesty · The Open Bioinformatics Journal · 1,152
Variant Review with the Integrative Genomics Viewer
2017 · James T. Robinson, Helga Thorvaldsdóttir, et al. · Cancer Research · 1,121
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
2014 · Andy Rimmer, Hang Phan, et al. · Nature Genetics · 1,057
Nextclade: clade assignment, mutation calling and quality control for viral genomes
2021 · Ivan Aksamentov, Cornelius Roemer, et al. · The Journal of Open Source Software · 1,051
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VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research
2016 · Zhongwu Lai, Aleksandra Markovets, et al. · Nucleic Acids Research · 969
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A primer on deep learning in genomics
2018 · James Zou, Mikael Huss, et al. · Nature Genetics · 890
Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations
2003 · Devin Dressman, Hai Yan, et al. · Proceedings of the National Academy of Sciences · 845
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
2014 · Justin M Zook, Brad Chapman, et al. · Nature Biotechnology · 815
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SomaticSniper: identification of somatic point mutations in whole genome sequencing data
2011 · David E. Larson, Christopher C. Harris, et al. · Bioinformatics · 661
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Works count: 11,410
Citation count: 257,000
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