Variant annotation tool

Question

[agata88]

Hi,

Do you know any tool like Annovar but with MIT licence? Or other licence that allows to use without academic email? I would appreciate for help, Best, Agata

[agata88]

Thanks Alon, Does this tool also annotate indels? Or should I use another tool for that? Best, Agata

[alons]

You're welcome! For small indels it will suffice. in their documentation they state that it can annotate some of the structural variants but the tool is mainly for SNPs and small indels from my experience.

For medium-large sized indels we're currently using VEP, highly recommended and it's open source: http://asia.ensembl.org/info/docs/tools/vep/index.html

[User 59]

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[agata88]

The SnpEff tool gets the output in vcf format, is there a possibility to get the output in for example csv file? With all the annotated fields? Or should I just write my own script to do that?

Best, Agata

Answer 1

[alons]

Hi Agata,

We're using the program SnpEff (Java based) for variant annotation, I highly recommend it for SNPs. It also comes with a program called SnpSift which allows you to annotate/intersect/join your variants with custom VCFs: http://snpeff.sourceforge.net/

If I remember correctly the license doesn't require an academic email.

Good luck! Alon

Answer 2

[Emily]

The Ensembl VEP requires no academic email or license – it's completely Open Source. It'll do SNPs, indels and structural variants.

[Neilfws]

nice REST interface too, a rare thing in bioinformatics

Answer 3

[Zaag]

I like KGGSEQ a lot for that: http://grass.cgs.hku.hk/limx/kggseq/