FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units

DeNovoGear: de novo indel and point mutation discovery and phasing

(2013) Avinash Ramu et al.   NATURE METHODS

Rare variant detection using family-based sequencing analysis

(2013) G. Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving sequence-based genotype calls with linkage disequilibrium and pedigree information

(2012) Baiyu Zhou et al.   Annals of Applied Statistics

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

(2012) Pooya Zandevakili et al.   PLoS One

A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

(2012) Bingshan Li et al.   PLoS Genetics

Chromosomal Haplotypes by Genetic Phasing of Human Families

(2011) Jared C. Roach et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The gputools package enables GPU computing in R

(2009) J. Buckner et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS