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