Question: Variant filtration software
0
gravatar for SunRise2019
7 weeks ago by
SunRise201910
SunRise201910 wrote:

Is there a freely available piece of software that can do variant filtration to identify possibly clinically relevant variants (SNVs, CNVs, Indels) from vcf files?

exome • 186 views
ADD COMMENTlink modified 7 weeks ago by Hamid Ghaedi1.2k • written 7 weeks ago by SunRise201910

Annotate the variants and then filter them accordingly. You can try SnpEff and SnpSift in combination.

ADD REPLYlink written 7 weeks ago by Arup Ghosh2.7k
2
gravatar for Hamid Ghaedi
7 weeks ago by
Hamid Ghaedi1.2k
Canada
Hamid Ghaedi1.2k wrote:

There are tools like ANNOVAR, SnpEff, and VEP that are widely used for variant annotation. Most variant filtration/prioritization software work on the output from these three main software. Appended below is a list of software that one can use to do variant annotation, filtration, and even prioritization.

NOTE: However you can use these free platforms in a clinical setting, they are designed for research use. In some cases, there is a clinical version available which is not free.

1- wANNOVAR: is a webtool for variant annotation, filtration, prioritization by Phenolyzer . This is an online version of the ANNOVAR .

2- GENEYX formerly known as TGex is a webtool for variant annotation by SnpEff, filtration, and prioritization (by VarElect)

3- VarAFT is a tool for variant annotation by ANNOVAR, filtration, and prioritization

4- SeattleSeq Annotation: is a webtool for ariant annotation.

5- Mendel,MD!: is a webtool for variant annotation, filtration and prioritization (?).

6- UCSC Variant Annotation Integrator

7- BrowseVCF: a web-application to quickly prioritize disease-causative variants in VCF files

8- Varsome: this is a variant classifiers based on ACMG2015

9- InterVar: variant classifiers

ADD COMMENTlink written 7 weeks ago by Hamid Ghaedi1.2k

Thanks! Very helpful!

ADD REPLYlink written 4 weeks ago by SunRise201910
1

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ADD REPLYlink written 4 weeks ago by Hamid Ghaedi1.2k
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