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Table 1 A descriptive summary of the variant calling pipelines included in the comparative analyses.

From: Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Pipeline name Alignment method Variant-calling module Description of variant-calling algorithm
SOAP SOAPaligner version 2.21/BWA version 0.5.9 SOAPsnp version 1.03/SOAPindel version 2.01 SOAP uses a method based on Bayes' theorem to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors [22].
GATK version 1.5 BWA version 0.5.9 UnifiedGenotyper version 1.5 GATK employs a general Bayesian framework to distinguish and call variants. Error correction models are guided by expected characteristics of human variation to further refine variant calls [19].
SNVer version 0.2.1 BWA version 0.5.9 SNVerIndiversion idual version 0.2.1 SNVer uses a more general frequentist framework, and formulates variant calling as a hypothesis-testing problem [25].
GNUMAP version 3.1.0 GNUMAP version 3.1.0 GNUMAP version 3.1.0 GNUMAP incorporates the base uncertainty of the reads into mapping analysis using a probabilistic Needleman-Wunsch algorithm [24].
SAMtools version 0.1.18 BWA version 0.5.9 mpileup version 0.1.18 SAMtools [20] calls variants by generating a consensus sequence using the MAQ model framework, which uses a general Bayesian framework for picking the base that maximizes the posterior probability with the highest Phred quality score.