SNVMix2 – Detect Single Nucleotide Variants from Next Generation Sequencing

SNVMix2

:: DESCRIPTION

SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes:  aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).  A tool for fitting the model using expectation maximization is also supplied (use -T option).

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNVMix

:: MORE INFORMATION

Citation

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Bioinformatics. 2010 Mar 15;26(6):730-6.

snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

Variant Tool Chest 0.9.3 alpha – Analyzing Variants

Variant Tool Chest 0.9.3 alpha

:: DESCRIPTION

The Variant Tool Chest (VTC) is designed to be a tool chest for analyzing variants (particularly VCF files)

::DEVELOPER

VTC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Java

:: DOWNLOAD

 Variant Tool Chest

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.
Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.
Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O’Fallon BD, Kauwe JS, Ridge PG.

ClinSeK 1.2e – Targeted Variant Characterization Framework for Clinical Sequencing

ClinSeK 1.2e

:: DESCRIPTION

ClinSeK is a targeted sequence analysis toolkit that allows quick and sensitive investigation of genetic variation at sites of interest from high-throughput sequencing data.

::DEVELOPER

ClinSeK team

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ClinSeK

:: MORE INFORMATION

Citation

ClinSeK: a targeted variant characterization framework for clinical sequencing.
Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K.
Genome Med. 2015 Mar 31;7(1):34. doi: 10.1186/s13073-015-0155-1.

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.

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.

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7 – Genome Aligner and Variant Caller

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7

:: DESCRIPTION

Isaac is ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. An ultrafast DNA sequence aligner /isaac_aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (isaac_variant_caller– Isaac Variant Caller) have been developed.

::DEVELOPER

Illumina, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Isaac

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):2041-3. doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.
Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW.

VarScan 2.4.0 – Variant Caller for Short Sequence Reads

VarScan 2.4.0

:: DESCRIPTION

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 VarScan

:: MORE INFORMATION

Citation:

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009).
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID:

HPG Variant 1.0 – Characterization of Variants found by Next-Generation Sequencing

HPG Variant 1.0

:: DESCRIPTION

The HPG Variant (VARIant ANalysis Tool) suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics.

::DEVELOPER

High Performance Genomics (HPG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  HPG Variant

:: MORE INFORMATION

Citation

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.
Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572.

FermiKit 0.13 – De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FermiKit

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.