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Deacon Sweeney edited this page Mar 7, 2018 · 36 revisions

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
msiseq 2015 MSI National Cancer Center Singapore 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
no name 2017 MSI classification Harvard Medical School study contact authors

STR Callers

caller orig pub class study source
STRetch 2017 str study source
hipSTR 2016 STR study source

Ion Torrent/454

caller orig pub class input study source
AIRVF 2017 DNA pyro filter study source
DUDE-Seq 2017 DNA pyro filter study source
NoDe 2015 DNA pyro filter study source
FlowCLUS 2015 RNA pyro filter study source
otg-snpcaller 2014 SNV torrent study available?
pyroHMMsnp 2013 SNV torrent/454 study source
pyroHMMvar 2013 indel torrent/454 study source
R453Plus1toolbox 2011 SNV 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UNPUBLISHED CALLERS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
concod 2016 sv conf.
cnndel 2016 sv conf.
needlestack 2016 SNVs and indels multi-sample BAMs source
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
sprites 2016 sv https://academic.oup.com/bioinformatics/article/32/12/1788/1743630/Sprites-detection-of-deletions-from-sequencing
splazers 2012 indel https://academic.oup.com/bioinformatics/article/28/5/619/248213/Detecting-genomic-indel-variants-with-exact
MindTheGap 2014 insertions c elegans https://academic.oup.com/bioinformatics/article/30/24/3451/2422179/MindTheGap-integrated-detection-and-assembly-of http://gatb.inria.fr/software/mind-the-gap/
Factera 2015 SV/fusion https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296148/ https://factera.stanford.edu/
dindel 2011 indels Sanger, slow http://europepmc.org/abstract/MED/20980555 N/A
piCALL 2011 indel scripps, exon https://www.ncbi.nlm.nih.gov/pubmed/21653520
svseq 1 & 2 2011 SV split-read https://www.ncbi.nlm.nih.gov/pubmed/21994222
Spanner 2011 SV https://www.ncbi.nlm.nih.gov/pubmed/21293372
SPLINTER 2010 SNV SNPSeeker + indels https://www.ncbi.nlm.nih.gov/pubmed/21041413/
bam2mpg 2010 SNV https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945191/
svmerge 2010
snvmix 2010 SNV early cancer-specific, with low purity expectations https://academic.oup.com/bioinformatics/article/26/6/730/245170/SNVMix-predicting-single-nucleotide-variants-from
cnD 2010 cnv https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820678/
dna sudoku 2009 SNV overlapping pooling design https://www.ncbi.nlm.nih.gov/pubmed/19447965/
breseq 2009 SNV binomial model https://www.researchgate.net/publication/232776704_Genome_evolution_and_adaptation_in_a_long-term_experiment_with_Escherichia_coli
maq 2009 SNV bayesian model includes sequencing errors https://www.ncbi.nlm.nih.gov/pubmed/18714091
SNPSeeker 2009 SNV pooling. compares observed allele frequencies against the distribution of sequencing errors as measured by the Kullback Leibler (KL) distance https://www.ncbi.nlm.nih.gov/pubmed/19252504/
modil 2009 indels http://www.nature.com/nmeth/journal/v6/n7/full/nmeth.f.256.html
VariationHunter 2009 SV http://genome.cshlp.org/content/19/7/1270.short
mrcanavar 2009 cnv https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875196/
maq 2008 SNV https://www.ncbi.nlm.nih.gov/pubmed/18714091
PEM 2007 SV paired-end http://science.sciencemag.org/content/318/5849/420
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/

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