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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...at the corresponding positions in the reference . This obscures accurate estimation of allele frequency and underestimates the real level of STR variation in the . To alleviate this problem, a short-read alignment approach using nonrepetitive flanks of STR-containing reads has been proposed recently (lobSTR) (Gymrek...
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Method: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
- Yi Wang,
- James Lu,
- Jin Yu,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112
...-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical...
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Resource: SOAPindel: Efficient identification of indels from short paired reads
- Shengting Li,
- Ruiqiang Li,
- Heng Li,
- Jianliang Lu,
- Yingrui Li,
- Lars Bolund,
- Mikkel H. Schierup,
- and Jun Wang
Genome Res. January 2013 23: 195-200; Published in Advance September 12, 2012, doi:10.1101/gr.132480.111
...compares indel calling on chromosome 7 with other methods (using their default settings). For all size classes, SOAPindel reports more indels, while GATK and Dindel find no indels, and Pindel finds no insertions larger than 19 bp in this data set, which is based on 40-bp read length. We used different...
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Research: The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
- Stephen B. Montgomery,
- David L. Goode,
- Erika Kvikstad,
- Cornelis A. Albers,
- Zhengdong D. Zhang,
- Xinmeng Jasmine Mu,
- Guruprasad Ananda,
- Bryan Howie,
- Konrad J. Karczewski,
- Kevin S. Smith,
- Vanessa Anaya,
- Rhea Richardson,
- Joe Davis,
- The 1000 Genomes Project Consortium,
- Daniel G. MacArthur,
- Arend Sidow,
- Laurent Duret,
- Mark Gerstein,
- Kateryna D. Makova,
- Jonathan Marchini,
- Gil McVean,
- and Gerton Lunter
Genome Res. May 2013 23: 749-761; Published in Advance March 11, 2013, doi:10.1101/gr.148718.112
...mapping all reads with Stampy (Lunter and Goodson 2011) and constructing a candidate set of indels as described above, we called sites and computed genotype likelihoods for each population separately using Dindel (Albers et al. 2011). Dindel also reports sites where evidence for multiple alleles...
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Resource: SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
- Si Quang Le and
- Richard Durbin
Genome Res. June 2011 21: 952-960; Published in Advance October 27, 2010, doi:10.1101/gr.113084.110
...sequencing. Nature 467: 1061–1073. Albers CA, Lunter G, MacArthur DG, McVean G, OuwehandWH, Durbin R. 2011. Dindel: Accurate indel calls from short-read data. Genome Res (this issue). doi: 10.1101/gr.112326.110 Browning BL, Yu Z. 2009. Simultaneous genotype calling and haplotype phasing improves genotype...
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Method: A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
- Daniel A. King,
- Tomas W. Fitzgerald,
- Ray Miller,
- Natalie Canham,
- Jill Clayton-Smith,
- Diana Johnson,
- Sahar Mansour,
- Fiona Stewart,
- Pradeep Vasudevan,
- Matthew E. Hurles,
- and the DDD Study
Genome Res. April 2014 24: 673-687; Published in Advance December 19, 2013, doi:10.1101/gr.160465.113
...sequencing of parent-offspring trios is a popular strategy for identifying causative genetic variants in children with rare diseases. This method owes its strength to the leveraging of inheritance information, which facilitates de novo variant calling, inference of compound heterozygosity...
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Research: Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles
- Tannistha Nandi,
- Matthew T.G. Holden,
- Xavier Didelot,
- Kurosh Mehershahi,
- Justin A. Boddey,
- Ifor Beacham,
- Ian Peak,
- John Harting,
- Primo Baybayan,
- Yan Guo,
- Susana Wang,
- Lee Chee How,
- Bernice Sim,
- Angela Essex-Lopresti,
- Mitali Sarkar-Tyson,
- Michelle Nelson,
- Sophie Smither,
- Catherine Ong,
- Lay Tin Aw,
- Chua Hui Hoon,
- Stephen Michell,
- David J. Studholme,
- Richard Titball,
- Swaine L. Chen,
- Julian Parkhill,
- and Patrick Tan
Genome Res. January 2015 25: 129-141; Published in Advance September 18, 2014, doi:10.1101/gr.177543.114
...was performed to obtain two circular contigs of 4.0 and 3.1 Mb (average GC content is 68%) with 2403 and 1473 post-filter base coverage, 213 and 223 preassembled read coverage, respectively (Chin et al. 2013). We identified a 12.4-kb plasmid in Bp35 called pBp35 that to our knowledge represents the first...
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Research: A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
- Matthew T.G. Holden,
- Li-Yang Hsu,
- Kevin Kurt,
- Lucy A. Weinert,
- Alison E. Mather,
- Simon R. Harris,
- Birgit Strommenger,
- Franziska Layer,
- Wolfgang Witte,
- Herminia de Lencastre,
- Robert Skov,
- Henrik Westh,
- Helena Žemličková,
- Geoffrey Coombs,
- Angela M. Kearns,
- Robert L.R. Hill,
- Jonathan Edgeworth,
- Ian Gould,
- Vanya Gant,
- Jonathan Cooke,
- Giles F. Edwards,
- Paul R. McAdam,
- Kate E. Templeton,
- Angela McCann,
- Zhemin Zhou,
- Santiago Castillo-Ramírez,
- Edward J. Feil,
- Lyndsey O. Hudson,
- Mark C. Enright,
- Francois Balloux,
- David M. Aanensen,
- Brian G. Spratt,
- J. Ross Fitzgerald,
- Julian Parkhill,
- Mark Achtman,
- Stephen D. Bentley,
- and Ulrich Nübel
Genome Res. April 2013 23: 653-664; Published in Advance January 8, 2013, doi:10.1101/gr.147710.112
...architecture of ST22-A, all ST22-A s possess five indels in the core , including a 2268-bp deletion in the fibronectinbinding protein (FnBP) locus (Supplemental Table S3). This FnBP deletion was caused by homologous recombination between the C-terminal region of fnbA and the N-terminal region of fnb...
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