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MSI CALLERS

Caller PubYear Specialty From Study Source
msisensor 2014 Microsatellite Instability(MSI) Memorial Sloan Kettering Cancer Center study source
msings 2014 MSI University of Washington, Seattle study source
msiplus 2015 MSI University of Washington, Seattle study uses msings
msiseq 2015 MSI National Cancer Center Singapore study source
mosaic 2016 MSI Howard Hughes Medical Institute study source
mirmmr 2017 MSI with methylation and mutation Siteman Cancer Center, Wash U in St. Louis study source
mantis 2017 MSI The Ohio State University study source
msi-coloncore 2017 MSI Zhejaing University, China study NA
no name 2017 MSI Harvard Medical School study contact authors
msipred 2018 MSI Miami University, Ohio study source

STR Callers

caller orig pub class study source
hipSTR 2016 STR study source

Ion Torrent/454

caller orig pub class input study source
otg-snpcaller 2014 SNV torrent study available?
R453Plus1toolbox 2011 SNV 454 study source
pyroHMMsnp 2013 SNV torrent/454 study source
pyroHMMvar 2013 indel torrent/454 study source

Nanopore

caller orig pub class input study source
graphmap 2016 SNV nanopore study source
marginAlign 2015 SNV nanopore study source

PacBio

caller orig pub class input study source
SMRT-SV 2016 SV pacbio study source
HySA 2017 SV/indel pacbio+illumina study source
Multibreak-SV 2014 SV PacBio study source
PBHoney 2014 SV PacBio study source

Bio Nano

caller orig pub class input study source
Parliament 2015 SV bio nano Illumina/PacBio/BioNano study

RNA

caller orig pub class input study source
eSNV-Detect 2014 eSNV rna study source
radia 2014 SNV/indel rna+dna study source
UNCeqR 2014 SNV/indel rna+dna study source
BreakTrans 2013 SV wgs+rna study source

de novo Filters

caller orig pub class input type study source
denovolyzer 2015 SNV/indel vcf de novo study
Triodenovo 2015 SNV vcfs germ study source
MendelScan 2014 SNV/indel vcfs exome germ study source
trioCaller 2013 SNV vcfs denovo study source
FamSeq 2012 SNV/indel vcf denovo study source
ForestDNM 2012 SNV/indel vcf denovo study source
Var-MD 2012 SNV/indel vcfs exome denovo study source
kggseq 2012 SNV mendel filter study

UNPUBLISHED CALLERS

caller release caller class input type study source
replow 2017 snv+indel background error correction preprint source
needlestack 2017 snv+indel multi-sample BAMs source
pisces 2017 snv+indel conf source
concod 2016 sv conf
cnndel 2016 sv conf
svmod 2016 sv open
UPS-indel 2016 indel conf source
BreakDown 2015 SV/VAF thesis
excaliburSMD 2014 source
takeabreak 2014 inv breakpoints conf source
QuadGT 2013 SNV exome trio conf source
SoapSNV 2013 multi source
CNValidator 2012 CNV source
mogul 2012 conf
SeqCNVCBS 2012 CNV source
bassovac 2011 source
kissnp 2010 open
glfTools 2010 SNV source
BREPA SV source
snippy source
copycat source

Unsorted Callers

caller orig pub caller class input type study source
PolyPhred 2006 SNV https://www.ncbi.nlm.nih.gov/pubmed/16493422/
SNPDetector 2005 SNV https://www.ncbi.nlm.nih.gov/pubmed/16261194/
novoSNP 2005 SNV https://www.ncbi.nlm.nih.gov/pubmed/15741513/
ssahaSNP 2001 SNV https://www.ncbi.nlm.nih.gov/pubmed/11591649/
polybayes 1999 SNV https://www.ncbi.nlm.nih.gov/pubmed/10581034/