User profiles for author:Erik author:Garrison

Erik Garrison

Wellcome Trust Sanger Institute (Cambridge University)
Verified email at
Cited by 12207

Haplotype-based variant detection from short-read sequencing

E Garrison, G Marth - arXiv preprint arXiv:1207.3907, 2012 -
Abstract: 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-

[HTML][HTML] An integrated map of structural variation in 2,504 human genomes

…, K Walter, S Meiers, S Kashin, E Garrison… - Nature, 2015 -
Summary Structural variants (SVs) are implicated in numerous diseases and make up the
majority of varying nucleotides among human genomes. Here we describe an integrated set
of eight SV classes comprising both balanced and unbalanced variants, which we

Demographic history and rare allele sharing among human populations

…, X Zheng, Y Zhou, EP Garrison… - Proceedings of the …, 2011 - National Acad Sciences
Abstract High-throughput sequencing technology enables population-level surveys of
human genomic variation. Here, we examine the joint allele frequency distributions across
continental human populations and present an approach for combining complementary

Integrative annotation of variants from 1092 humans: application to cancer genomics

…, US Evani, P Flicek, R Fragoza, E Garrison… - …, 2013 -
Methods We investigated patterns of selection in DNA elements from the ENCODE project
using the full spectrum of variants from 1092 individuals in the 1000 Genomes Project
(Phase 1), including single-nucleotide variants (SNVs), short insertions and deletions

BamTools: a C++ API and toolkit for analyzing and managing BAM files

DW Barnett, EK Garrison, AR Quinlan… - …, 2011 -
Abstract Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use
access to alignment results and flexible data management tools (eg filtering, merging,
sorting, etc.). However, the enormous amount of data produced by current sequencing

[HTML][HTML] A comprehensive map of mobile element insertion polymorphisms in humans

…, WP Lee, M Busby, AR Indap, E Garrison… - PLoS …, 2011 -
Abstract As a consequence of the accumulation of insertion events over evolutionary time,
mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA
mobile element families are still duplicating, generating variation between individual

[HTML][HTML] MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping

…, MP Stromberg, A Ward, C Stewart, EP Garrison… - PloS one, 2014 -
Abstract MOSAIK is a stable, sensitive and open-source program for mapping second and
third-generation sequencing reads to a reference genome. Uniquely among current
mapping tools, MOSAIK can align reads generated by all the major sequencing

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

…, GRS Ritchie, E Cerveira, TW Fitzgerald, E Garrison… - Nature …, 2016 -
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26
worldwide populations by the 1000 Genomes Project. We discovered more than 65,000
variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and

[HTML][HTML] SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications

M Zhao, WP Lee, EP Garrison, GT Marth - PloS one, 2013 -
Background The Smith-Waterman algorithm, which produces the optimal pairwise alignment
between two sequences, is frequently used as a key component of fast heuristic read
mapping and variation detection tools for next-generation sequencing data. Though various

[HTML][HTML] SpeedSeq: ultra-fast personal genome analysis and interpretation

…, GG Faust, MR Lindberg, DB Rose, EP Garrison… - Nature …, 2015 -
Abstract SpeedSeq is an open-source genome analysis platform that accomplishes
alignment, variant detection and functional annotation of a 50× human genome in 13 hours
on a low-cost server, alleviating a bioinformatics bottleneck that typically demands weeks of