| VarScan |
http://varscan.sourceforge.net/ |
SNP detection |
[62] |
| ProbHD |
http://seqanswers.com/wiki/ProbHD |
SNP detection |
[64] |
| Atlas-SNP2 |
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc |
SNP detection |
[54] |
| NA |
ftp://ftp.sanger.ac.uk/pub/pathogens/pools/ |
allele frequency estimation |
[72] |
| NA |
http://www.genetics.org/content/suppl/2009/03/16/genetics.109.100479.DC1 |
allele frequency estimation |
[73] |
| MapNext |
http://evolution.sysu.edu.cn/english/software/mapnext.htm |
allele frequency estimation |
[74] |
| testassoc |
http://www.biomedcentral.com/1471-2105/12/231/additional |
allele frequency estimation |
[75] |
| SNVer |
http://snver.sourceforge.net/ |
SNP detection and allele frequency estimation |
[76] |
| samtools |
http://samtools.sourceforge.net/ |
genotype calling (both SS & MS-SS) |
[31] |
| GATK |
http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit |
genotype calling (both SS & MS-SS) |
[50] |
| SOAP-SNP |
http://soap.genomics.org.cn/soapsnp.html |
genotype calling (both SS & MS-SS) |
[78] |
| glfMultiples |
http://genome.sph.umich.edu/wiki/GlfMultiples |
genotype calling (both SS & MS-SS) |
[87] |
| SNIP-Seq |
http://polymorphism.scripps.edu/~vbansal/software/SNIP-Seq/ |
MS-SS genotype calling |
[80] |
| SeqEM |
http://hihg.med.miami.edu/software-download/seqem-version-1.0 |
MS-SS genotype calling |
[83] |
| MARGARITA + QCALL |
ftp://ftp.sanger.ac.uk/pub/rd/QCALL |
MS-LD genotype calling |
[84, 85] |
| GATK + BEAGLE |
http://faculty.washington.edu/browning/beagle/beagle.html |
MS-LD genotype calling |
[50, 86] |
| thunder |
http://genome.sph.umich.edu/wiki/Thunder |
MS-LD genotype calling |
[87] |
| SNPTools |
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_snp_tools-ti.hgsc |
MS-LD genotype calling |
NA |
