MCV – Mutation Calling with VAF for Whole Genome Sequencing

MCV

:: DESCRIPTION

MCV is a pipeline to identify somatic substitutions and indels with VAF (variant allele frequency) from whole genome sequencing

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MCV

:: MORE INFORMATION

Indexcov – Fast Coverage Quality Control for Whole-genome Sequencing

Indexcov

:: DESCRIPTION

Indexcov is an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.

::DEVELOPER

The Quinlan Lab , Ira Hall Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Indexcov

:: MORE INFORMATION

Citation:

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.
Indexcov: fast coverage quality control for whole-genome sequencing.
Pedersen BS1,2, Collins RL3,4,5, Talkowski ME3,6,4,5, Quinlan AR

RareVariantVis 1.6.2 – Visualization of Rare Variants in Whole Genome Sequencing data

RareVariantVis 1.6.2

:: DESCRIPTION

RareVariantVis is a new tool for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants.

::DEVELOPER

Tomasz Stokowy <tomasz.stokowy at k2.uib.no>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RareVariantVis

:: MORE INFORMATION

Citation

RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM.
Bioinformatics. 2016 Jun 10. pii: btw359.

MarViN 0.1.0 – Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distribution

MarViN 0.1.0

:: DESCRIPTION

MarViN is an algorithm that models  linkage-disequilibrium (LD) using a simple multivariate Gaussian distribution.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MarViN

:: MORE INFORMATION

Citation:

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.
Arthur R, O’Connell J, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2016 Mar 9. pii: btw097

gSearch – Search tool for Whole-genome Sequencing

gSearch

:: DESCRIPTION

gSearch is a fast and flexible general search tool for whole-genome sequencing

::DEVELOPER

Soongsil University Machine Learning Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MacOsX

:: DOWNLOAD

 gSearch

:: MORE INFORMATION

Citation

gSearch: a fast and flexible general search tool for whole-genome sequencing.
Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW.
Bioinformatics. 2012 Aug 15;28(16):2176-7. doi: 10.1093/bioinformatics/bts358

MegaMapper 1.01e – Software for Positional Cloning of Mutations by Whole Genome Sequencing

MegaMapper 1.01e

:: DESCRIPTION

MegaMapper is a computational pipeline for positional cloning of mutations by whole genome sequencing.

::DEVELOPER

the Megason Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MegaMapper

:: MORE INFORMATION

Citation

Development. 2012 Nov;139(22):4280-90. doi: 10.1242/dev.083931. Epub 2012 Oct 10.
Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing.
Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, Nicolson T, Megason SG.

BIC-seq 2.1.1 – Copy Number analysis from Whole-genome Sequencing data

BIC-seq 2.1.1

:: DESCRIPTION

BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome.

::DEVELOPER

Peter J.Park

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package / Perl

:: DOWNLOAD

 BIC-seq

:: MORE INFORMATION

Citation

Xi et al,
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
PNAS, 2011 November 15, 2011 vol. 108 no. 46