SNP Discovery through Next-Generation Sequencing and Its Applications
Table 2
Commonly used NGS variant calling software. Download information for these software is compiled in Table 4. A more comprehensive list of variant calling programs is available at http://seqanswers.com/wiki/Software/list.
Software
Multisample support
Reference
Features
Platform
Samtools
Yes
Aligned reads
Include computation of genotype likelihoods and variant calling
Linux
SOAPsnp
No
Variant database
Part of SOAP3 for variant calling
Linux
GATK
Yes
Aligned reads
Include variant caller, SNP filter, and SNP quality calibrator
Linux
SNVer
Yes
Aligned reads
Fast variant caller, assigning SNP significance based on read depth
Windows, Linux, Mac OS X
SHORE
Yes
Aligned reads
Variant calling based on reference sequence even from other species
Linux, Mac OS X
MaCH
Yes
Genotype likelihoods
Variant calling with or without LD information
Windows, Linux, Mac OSX
IMPUTE2
Yes
Candidate SNPs and genotype likelihoods
Variant calling and linkage map-based SNP imputation
