Table 1. A list of available non-commercial NGS genotype-calling software.
| Software | Available from | Calling method | Prerequisites | Comments | Refs |
|---|---|---|---|---|---|
| SOAP2 | http://soap.genomics.org.cn/index.html | Single-sample | High-quality variant database (for example, dbSNP) | Package for NGS data analysis, which includes a single individual genotype caller (SOAPsnp) | 15 |
| realSFS | http://128.32.118.212/thorfinn/realSFS/ | Single-sample | Aligned reads | Software for SNP and genotype calling using single individuals and allele frequencies. Site frequency spectrum (SFS) estimation | - |
| Samtools | http://samtools.sourceforge.net/ | Multi-sample | Aligned reads | Package for manipulation of NGS alignments, which includes a computation of genotype likelihoods (samtools) and SNP and genotype calling (bcftools) | 53 |
| GATK | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit | Multi-sample | Aligned reads | Package for aligned NGS data analysis, which includes a SNP and genotype caller (Unifed Genotyper), SNP filtering (Variant Filtration) and SNP quality recalibration (Variant Recalibrator) | 32,33 |
| Beagle | http://faculty.washington.edu/browning/beagle/beagle.html | Multi-sample LD | Candidate SNPs, genotype likelihoods | Software for imputation, phasing and association that includes a mode for genotype calling | 42 |
| IMPUTE2 | http://mathgen.stats.ox.ac.uk/impute/impute_v2.html | Multi-sample LD | Candidate SNPs, genotype likelihoods | Software for imputation and phasing, including a mode for genotype calling. Requires fine-scale linkage map | 44 |
| QCall | ftp://ftp.sanger.ac.uk/pub/rd/QCALL | Multi-sample LD | ‘Feasible’ genealogies at a dense set of loci, genotype likelihoods | Software for SNP and genotype calling, including a method for generating candidate SNPs without LD information (NLDA) and a method for incorporating LD information (LDA). The ‘feasible’ genealogies can be generated using Margarita (http://www.sanger.ac.uk/resources/software/margarita) | 54 |
| MaCH | http://genome.sph.umich.edu/wiki/Thunder | Multi-sample LD | Genotype likelihoods | Software for SNP and genotype calling, including a method (GPT_Freq) for generating candidate SNPs without LD information and a method (thunder_glf_freq) for incorporating LD information | - |
A more complete list is available from http://seqanswers.com/wiki/Software/list. LD, linkage disequilibrium; NGS, next-generation sequencing.