Variant Callers for Next-Generation Sequencing Data: A Comparison Study

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach

(2012) Swetansu Pattnaik et al.   PLoS One

Improving bioinformatic pipelines for exome variant calling

(2012) Hanlee P Ji   Genome Medicine

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evaluation of next-generation sequencing software in mapping and assembly

(2011) Suying Bao et al.   JOURNAL OF HUMAN GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

(2010) E. R. Martin et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH