caller class
input type
somatic/denovo
from
validated vs.
cited
used by
compared by
algorithm
features
description
installation
study
source
notes
ioncopy
2016
cna
amplicon
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914355/
https://cran.r-project.org/web/packages/ioncopy/index.html
srbreak
2016
cna
read depth/split read
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023681/
https://github.com/hoangtn/SRBreak
m-hmm
2016
cnv
http://onlinelibrary.wiley.com/doi/10.1111/anzs.12175/full
NIKS
2013
SNV
https://www.ncbi.nlm.nih.gov/pubmed/23475072
oncosnpseq
2013
CNV/LOH
https://www.ncbi.nlm.nih.gov/pubmed/23926227
matchclip
2013
cnv
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744852/
cops
2012
cnv
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047812
seqcbs
2012
cnv
https://projecteuclid.org/euclid.aoas/1339419604
hugeseq
2012
sv
simple meta
http://www.nature.com/nbt/journal/v30/n3/abs/nbt.2134.html
svm2
2012
sv
kggseq
2012
SNV
mendelian
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326332/
dindel avail?
2011
indels
Sanger, slow
http://europepmc.org/abstract/MED/20980555
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/
snvmix
2010
SNV
early cancer-specific, with low purity expectations
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
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