FMFilter 1.0 – A Fast Model based Variant Filtering tool

FMFilter 1.0

:: DESCRIPTION

FMFilter (Fast Model based Filter) is an efficient filtering tool for next generation sequencing data produced by genetic disease studies.

::DEVELOPER

Advanced Genomics and Bioinformatic Research Group, İGBAM

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

  FMFilter

:: MORE INFORMATION

Citation

Akgün M, Faruk Gerdan Ö, Görmez Z, Demirci H.
FMFilter: A fast model based variant filtering tool.
J Biomed Inform. 2016 Apr;60:319-27. doi: 10.1016/j.jbi.2016.02.013. Epub 2016 Feb 27. PMID: 26925517.

Srfim 0.0-95 – Short-Read Filtering and Intensity-Modeling

Srfim 0.0-95

:: DESCRIPTION

Srfim does model-based quality assessment and base-calling for Illumina GA second-generation sequencing data.

::DEVELOPER

Héctor Corrada Bravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 Srfim

:: MORE INFORMATION

Citation:

H. Corrada Bravo, R.A. Irizarry.
Model-based quality assessment and base-calling for second-generation sequencing data” (Novmeber 2009).
Biometrics. Published online before print, Novemeber 13, 2009. doi10.1111/j.1541-0420.2009.01353.x

Mendelian – Heuristic Variant Filtering

Mendelian

:: DESCRIPTION

Mendelian is an R package that can be used to filter sequencing variants. It enables filtering for both dominant and recessive traits, with a wide variety of options (including reduced penetrance and detectance).

::DEVELOPER

Mendelian team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 Mendelian

:: MORE INFORMATION

Citation

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.
Broeckx BJ, Coopman F, Verhoeven G, Bosmans T, Gielen I, Dingemanse W, Saunders JH, Deforce D, Van Nieuwerburgh F.
BMC Bioinformatics. 2015 Nov 19;16:391. doi: 10.1186/s12859-015-0822-7.

gffread v0.12.2 – Filtering, Converting and Manipulating GFF files

gffread v0.12.2

:: DESCRIPTION

The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffread

:: MORE INFORMATION

Citation

Pertea G, Pertea M.
GFF Utilities: GffRead and GffCompare.
F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.

VariantBam 1.4.3 – Filtering and Profiling of Next-generational Sequencing data using Region-specific Rules

VariantBam 1.4.3

:: DESCRIPTION

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files.

::DEVELOPER

VariantBam team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 VariantBam

:: MORE INFORMATION

Citation:

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.
Wala J, Zhang CZ, Meyerson M, Beroukhim R.
Bioinformatics. 2016 Feb 26. pii: btw111.

Reaper 17-257 – Demultiplexing, Trimming and Filtering Short Read Sequencing data

Reaper 17-257

:: DESCRIPTION

Reaper is a program for demultiplexing, trimming and filtering short read sequencing data. It is intended to be suitable for dealing with a wide range of sequencing protocols, and will be updated to support new protocols where the current set of features does not suffice

::DEVELOPER

Stijn van Dongen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • C Compiler

:: DOWNLOAD

 Reaper

:: MORE INFORMATION

TrioVis 20130409 – Visualization approach for Filtering Genomic Variants of Parent-child Trios

TrioVis 20130409

:: DESCRIPTION

TrioVis is a visualisation tool developed to assist filtering on coverage and variant frequency for genomic variants from exome sequencing of parent-child trios. It organises the variant data by grouping each variant based on the laws of Mendelian inheritance. Taking three Variant Call Format (VCF) files as input, the tool provides a user interface to test different coverage thresholds (i.e. different levels of stringency), to find the optimal threshold values, and to gain insights into the global effects of filtering.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

TrioVis

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

TrioVis

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1801-2. doi: 10.1093/bioinformatics/btt267. Epub 2013 May 8.
TrioVis: a visualization approach for filtering genomic variants of parent-child trios.
Sakai R, Sifrim A, Vande Moere A, Aerts J.