KnockoffZoom 1.0 / KnockoffGWAS – multi-resolution Localization of causal Variants across the Genome

KnockoffZoom 1.0 / KnockoffGWAS

:: DESCRIPTION

KnockoffZoom localizes causal variants precisely and provably controls the false discovery rate using artificial genotypes as negative controls.

KnockoffGWAS is a powerful and versatile statistical method for the analysis of genome-wide association data with population structure.

::DEVELOPER

the Sabatti Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOSX / Linux

:: DOWNLOAD

KnockoffZoom / KnockoffGWAS

:: MORE INFORMATION

Citation

Sesia M, Katsevich E, Bates S, Candès E, Sabatti C.
Multi-resolution localization of causal variants across the genome.
Nat Commun. 2020 Feb 27;11(1):1093. doi: 10.1038/s41467-020-14791-2. Erratum in: Nat Commun. 2020 Apr 7;11(1):1799. PMID: 32107378; PMCID: PMC7046731.

MEGA-V – Mutation Enrichment Gene set Analysis of Variants

MEGA-V

:: DESCRIPTION

MEGA-V is an open-source R application with a Shiny web interface. It identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to (1) a control cohort (cohort B) or (2) a random distribution generated using Monte Carlo.

::DEVELOPER

the Ciccarelli Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
R

:: DOWNLOAD

MEGA-V

:: MORE INFORMATION

Citation:

Gambardella G, Cereda M, Benedetti L, Ciccarelli FD.
MEGA-V: detection of variant gene sets in patient cohorts.
Bioinformatics. 2017 Apr 15;33(8):1248-1249. doi: 10.1093/bioinformatics/btw809. PMID: 28003259; PMCID: PMC5408849.

RSVP – RNA-seq Variant Prediction

RSVP

:: DESCRIPTION

RSVP is a software package for prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads. The method is based on the use of ORF graphs, which are more general than the splice graphs used in traditional transcript assembly.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

RSVP

:: MORE INFORMATION

Citation

Improved transcript isoform discovery using ORF graphs.
Majoros WH, Lebeck N, Ohler U, Li S.
Bioinformatics. 2014 Apr 21.

FamSeq 1.0.3 – Calculating Probability of Variants in Family-based Sequencing data

FamSeq 1.0.3

:: DESCRIPTION

FamSeq (Family-Based Sequencing) is a computational tool for calculating probability of variants in family-based sequencing data.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /MacOsX/Windows
C++ Compiler

:: DOWNLOAD

FamSeq

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3985-90. doi: 10.1073/pnas.1222158110.
Rare variant detection using family-based sequencing analysis.
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W.

vipR 0.0.16 – Variant Identification in pooled DNA using R

vipR 0.0.16

:: DESCRIPTION

vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

::DEVELOPER

André Altmann

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

vipR

:: MORE INFORMATION

Citation

vipR: variant identification in pooled DNA using R.
Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B.
Bioinformatics. 2011 Jul 1;27(13):i77-84. doi: 10.1093/bioinformatics/btr205.

eSNV-Detect v1.0 – Reliable Identification of Variants Using RNA-seq Data

eSNV-Detect v1.0

:: DESCRIPTION

The eSNV-Detect is a method to detect expressed single nucleotide variants (eSNVs) with high specificity and sensitivity from the high throughput transcriptome sequencing data. Alignments from multiple aligers are used to cover the aligner bias and multiple genomic features are used to improve the specificity. For the expressed SNVs detected, it can also identify the amino acid change and classify the protein domains.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Virtual Box
R package

:: DOWNLOAD

eSNV-Detect

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct 28. pii: gku1005.
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Tang X, Baheti S1, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR

FAVR 1.0 – Filtering and Annotation of Variants that are Rare

FAVR 1.0

:: DESCRIPTION

FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python
PySam

:: DOWNLOAD

FAVR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 25;14:65. doi: 10.1186/1471-2105-14-65.
FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.
Pope BJ1, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ.

ROVER 2.0.0 / UNDR ROVER 2.0.0 – Read Overlap Variant Caller

ROVER 2.0.0 / UNDR ROVER 2.0.0

:: DESCRIPTION

ROVER is a read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets

UNDR ROVER (Unmapped Primer directed read overlap Variant caller) is an improved version of our ROVER variant calling tool for targeted DNA sequencing.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

ROVER , UNDR ROVER

:: MORE INFORMATION

Citation:

UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing.
Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ.
BMC Bioinformatics. 2016 Apr 16;17(1):165. doi: 10.1186/s12859-016-1014-9.

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3. doi: 10.1186/1751-0473-9-3.

NanoCaller 0.3.3 – Variant Calling tool for long-read Sequencing data

NanoCaller 0.3.3

:: DESCRIPTION

NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data. NanoCaller uses long-range haplotype structure to generate predictions for each SNP candidate variant site by considering pileup information of other candidate sites sharing reads. Subsequently, it performs read phasing, and carries out local realignment of each set of phased reads and the set of all reads for each indel candidate variant site to generate indel calling, and then creates consensus sequences for indel sequence prediction.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Pyton

:: DOWNLOAD

NanoCaller

:: MORE INFORMATION

Citation

Ahsan, Umair and Liu, Qian and Wang, Kai.
NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks.
bioRxiv 2019.12.29.890418; doi: https://doi.org/10.1101/2019.12.29.890418

VarMatch – Matching Variants in VCF files

VarMatch

:: DESCRIPTION

VarMatch: robust matching of small variant datasets using flexible scoring schemes

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

VarMatch

:: MORE INFORMATION

Citation:

Bioinformatics, 33 (9), 1301-1308 2017 May 1
VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes
Chen Sun , Paul Medvedev