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

LARVA – Large-scale Analysis of Variants in noncoding Annotations

LARVA

:: DESCRIPTION

LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LARVA

:: MORE INFORMATION

Citation:

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M.
Nucleic Acids Res. 2015 Sep 30;43(17):8123-34. doi: 10.1093/nar/gkv803.

Exomiser 12.1.0 – Annotates Variants from Whole-exome Sequencing Data

Exomiser 12.1.0

:: DESCRIPTION

The Exomiser is a Java program that functionally annotates and prioritises variants from whole-exome sequencing data starting from a VCF file.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 Exomiser

:: MORE INFORMATION

Citation

Improved exome prioritization of disease genes through cross-species phenotype comparison.
Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D.
Genome Res. 2014 Feb;24(2):340-8. doi: 10.1101/gr.160325.113.

VCMM 1.0.2 – Variant Caller with Multinomial probabilistic Model

VCMM 1.0.2

:: DESCRIPTION

VCMM is a tool for the detection of SNVs and INDELs based on a multinomial probabilistic method.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VCMM

:: MORE INFORMATION

Citation

Sci Rep. 2013;3:2161. doi: 10.1038/srep02161.
A practical method to detect SNVs and indels from whole genome and exome sequencing data.
Shigemizu D1, Fujimoto A, Akiyama S, Abe T, Nakano K, Boroevich KA, Yamamoto Y, Furuta M, Kubo M, Nakagawa H, Tsunoda T.