orig pub
caller class
input type
somatic/denovo
from
validated vs.
cited
used by
compared by
algorithm
features
description
installation
study
source
msisensor
2014
MSI instability
somatic
15
computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired
https://github.com/ding-lab/msisensor
hipSTR
2016
STR
polymut
0
haplotype
STR
a novel haplotype-based method for robustly genotyping, haplotyping, and phasing STRs from whole genome sequencing data
http://www.biorxiv.org/content/early/2016/09/27/077727
https://hipstr-tool.github.io/HipSTR/
otg-snpcaller (available?)
2014
torrent
8
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097507
available?
R453Plus1toolbox
2011
454
18
http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html
eSNV-Detect
2014
eSNV
rna-only
9
http://bioinformaticstools.mayo.edu/research/esnv-detect/
graphmap
2016
SNV
nanopore
8
http://www.nature.com/articles/ncomms11307
https://github.com/benedictpaten/marginAlign/blob/master/src/margin/marginCaller.py
marginAlign
2015
SNV
nanopore
149
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907500/
https://github.com/benedictpaten/marginAlign
radia
2014
SNV/indel
rna & dna
12
The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111516
https://github.com/aradenbaugh/radia/
UNCeqR
2014
SNV/indel
rna & dna
20
Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES.
https://academic.oup.com/nar/article/42/13/e107/1277201/Integrated-RNA-and-DNA-sequencing-improves
http://lbg.med.unc.edu/~mwilkers/unceqr_dist/
pyroHMMvar
2013
SNV/indel
torrent/454
Tsinghua U, Beijing
6
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888126/
https://github.com/homopolymer/PyroTools/
HySA (HybridAssemblySV)
2017
SV/indel
pacbio + illumina
0
best for long insertions, small indels, STR changes
Integrates sequencing reads from next-generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance assembly of structurally altered regions in human genome.
http://genome.cshlp.org/content/early/2017/01/19/gr.214767.116.abstract#corresp-1
https://bitbucket.org/xianfan/hybridassemblysv
Parliament
2015
SV
bio nano
Baylor, Gibbs
37
BioNano assembly
Integrates Illumina, PacBio, BioNano reads
adds bio nano
https://www.ncbi.nlm.nih.gov/pubmed/25886820
https://sourceforge.net/projects/parliamentsv/
Multibreak-SV
2014
SV
PacBio
Brown U, Raphael
15
parallel probablistic model
Pac Bio
combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253835/
https://github.com/raphael-group/multibreak-sv
PBHoney
2014
SV
PacBio
Baylor, Reid
16
interrupted mapping and intra-read discordance
Pac Bio
effective at detecting larger structural variants using whole-genome Pacific Biosciences RS II Continuous Long Reads
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-180
https://sourceforge.net/projects/pb-jelly/
BreakTrans
2013
SV
wgs/rna-seq
somatic
Wash U St Louis, Ding
10
limits breakpoint graph to transcribed regions
adds RNA-seq data
systematically maps predicted gene fusions to structural rearrangements
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-8-r87
http://bioinformatics.mdanderson.org/main/BreakTrans
MindTheGap
2014
insertions
c elegans
19
http://gatb.inria.fr/software/mind-the-gap/
Factera
2015
SV
Stanford, Alizadeh
11
fusion detection. soft-clip, kmer
trained on real tumor data
Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296148/
De novo Filters
denovolyzer
2015
SNV/indel
vcf
de novo
12
de novo filter
implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4606471/
Triodenovo (former polymutt)
2015
SNV
vcfs
germ
Vanderbilt, Li
denovogear
8
bayesian with flexible post hoc priors
works well for low coverage
disentangles prior mutation rates from evaluation of the likelihood of the data so that flexible priors can be adjusted post-hoc at different genomic sites
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410659/
http://genome.sph.umich.edu/wiki/Triodenovo#Download
MendelScan
2014
SNV/indel
vcfs exome
germ
U Texas
Inginuity Variant Analysis (Qiagen)
21
calls haplotypes, prioritizes variants using fam/pop data
exome
two complementary approaches. identifies segments of maximum identity by descent among affected individuals; nominates regions on the basis of shared rare variants and the absence of homozygous differences between affected individuals.
https://www.ncbi.nlm.nih.gov/pubmed/24560519
https://github.com/genome/mendelscan
trioCaller
2013
SNV
vcfs
denovo
34
HMM
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530674/
http://genome.sph.umich.edu/wiki/TrioCaller
FamSeq
2012
SNV/indel
vcf
denovo
U Texas MD Anderson Cancer Center
gatk, samtools mpileup both unfiltered
24
Bayesian network/markov chain-monte carlo
provides a confidence measure for variant calls using data from all family members and builds on Bayesian networks (13) and the Markov chain Monte Carlo (MCMC) algorithm
family-based variant calling program that provides a confidence measure for variant calls using data from all family members and builds on Bayesian networks and the Markov chain Monte Carlo (MCMC) algorithm
http://www.pnas.org/content/110/10/3985.long
http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html
ForestDNM
2012
SNV/indel
vcf
denovo
236
de novo filter
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712641/
http://sebatlab.ucsd.edu/index.php/software-data
Var-MD (available?)
2012
SNV/indel
vcfs exome
denovo
NHGRI, Boerkoel
n/a
22
variety of mendelian/quality filters
sorts variants by disease likelihood
generates a ranked list of variants using predicted pathogenicity, Mendelian inheritance models, genotype quality and population variant frequency data.