More.md

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UNPUBLISHED CALLERS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/