Table 4 Characteristics of several popular SNP callers for reference-mapped data

From: From next-generation resequencing reads to a high-quality variant data set

Software

Method

Sample

Reference

Atlas-SNP2

Bayesian

Single

Challis et al. (2012)

CRISP

Testing

Pooled

Bansal (2010)

Dindel

Hidden Markov model

Pooled

Albers et al. (2011)

FreeBayes

Bayesian

Multiple

NA

GATK

Bayesian

Multiple

McKenna et al, (2010)DePristo et al. (2011) Van der Auwera et al. (2013)

QCALL

Bayesian

Multiple

Le and Durbin (2011)

SAMtools

Bayesian

Multiple

Li et al. (2009a)

SeqEM

Bayesian

Multiple

Martin et al. (2010)

SLIDERII

Counting

Single

Malhis and Jones (2010)

SNP-o-matic

Counting

Single

Manske and Kwiatkowski (2009b)

SNVer

Testing

Single and pooled

Wei et al. (2011)

SOAPsnp

Bayesian

Single

Li et al. (2009b)

SYZYGY

Bayesian

Pooled

NA

  1. Abbreviations: NA, no publication available; SNP, single-nucleotide polymorphism.
  2. Popularity was assessed by the number of citations of the software.
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