Variant filtration software

Question

[SunRise2019]

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?

[Arup Ghosh]

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

Answer 1

[Hamid Ghaedi]

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 ANNOVAR annotated variants , filtration, and prioritization

4- SeattleSeq Annotation: is a webtool for variant 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 based on ACMG 2015 gudie line

10- seqr: a web-tool for rare disease genomics from Broad Institute (added on July 12,2021 suggested by Charlie2 )

11- The Exomiser : It prioritizes based on variant allele frequency, predicted pathogenicity and patient's phenotype (HPO terms) and also accepts family vcfs (so does segregation) (added on Aug 13,2021 suggested by @sh shruti.marwaha)

[SunRise2019]

Thanks! Very helpful!

[Hamid Ghaedi]

If you found this helpful, please upvote and whether this is a sort of answer for your question please approve the answer.

Answer 2

[Charlie2]

Might be too late for this to be of use now but I'd recommend seqr from the Broad Institute. Combines various prediction and annotation tools, powerful filtering options, also user-friendly and actively maintained.

Answer 3

[shruti.marwaha]

Exomiser is another great tool. https://github.com/exomiser/Exomiser It prioritizes based on variant allele frequency, predicted pathogenicity and patient's phenotype (HPO terms) and also accepts family vcfs (so does segregation).