Concepedia

Indel variant analysis of short-read sequencing data with Scalpel

Han Fang, Ewa A. Bergmann, Kanika Arora, Vladimir Vacic, Michael C. Zody, Ivan Iossifov, Jason O'Rawe, Yiyang Wu, Laura T. Jiménez Barrón, Julie Rosenbaum,

Nature Protocols · 2016 · 137 citations · 47 references

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47

The Sequence Alignment/Map format and SAMtools

Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text

, , +17

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text

, , +14

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

Kai Wang, Man Li, Håkon Håkonarson · Nucleic Acids Research · 2010 · 15.6K citations · Full text

, , +17

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

Pablo Cingolani, Adrian E. Platts, Le Lily Wang et al. · Fly · 2012 · 12.7K citations · Full text

, , +17

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

Mark A. DePristo, Eric Banks, Ryan Poplin et al. · Nature Genetics · 2011 · 12.4K citations · Full text

, , +14