Haplotype-based variant detection from short-read sequencing

By Erik P. Garrison, Gabor T. Marth. 2012

4,999 citations recorded by the source corpus.

The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4fab3a273af553b17bb099baa0eca3ce6e67f42b

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In Molecular Biology

1. Heng Li
2. Adam M. Phillippy
3. Sergey Koren
4. Steven L. Salzberg
5. Todd J. Treangen
6. Daniel C. Koboldt
7. Jared T. Simpson
8. Evan E. Eichler

Citations in the corpus

• A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree (2016, neutral): “We included variant calls from six different informatics pipelines (Conrad et al. 2011; Garrison and Marth 2012; Iqbal et al. 2012; Saunders et al. 2012; Raczy et al. 2013; Rimmer et al. 2014) and two different sequencing technologies (Bentley et al. 2008; Drmanac et al. 2010).”
• The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, methodology): “Here, we have taken a small step in that direction by identifying low quality bases, as computed by FreeBayes [54].”
• Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020, methodology): “Base pair errors were called using Free-Bayes [47] v1.”
• Toward better understanding of artifacts in variant calling from high-coverage samples (2014, methodology): “We called SNPs and short INDELs with FreeBayes (Garrison and Marth, 2012), GATK UnifiedGenotyper, Platypus, SAMtools and GATK HaplotypeCaller.”
• Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes (2020, background): “Phasing can be performed following three broad strategies: read-based phasing 18 , which assesses whether nearby variants co-segregate on the same reads in DNA sequencing data; family-based phasing 19 , which assesses whether pairs of variants are co-inherited within families; and population-based…”
• Real-time, portable genome sequencing for Ebola surveillance (2016, background): “England, Porton Down, Wiltshire SP4 0JG, UK (12)Friedrich-Loeffler-Institute, Greifswald, Germany (13)Spiez Laboratory, Spiez, Switzerland (14)Janssen-Cilag, Stockholm, Sweden (15)Public Health Agency of Canada, Winnipeg, Canada (16)Institut Pasteur Dakar, Dakar, Senegal (17)Laboratoire de Fièvres H”
• A universal SNP and small-indel variant caller using deep neural networks (2018, methodology): “We then applied the same dataset and evaluation methodology to a variety of both recent and commonly used bioinformatics methods, including the GATK, FreeBayes 22 , SAMtools 23 , 16GT 24 and Strelka 25 ( Table 1 ).”