how to annotate somatic mutation？

[zhaopeihua]

hi：
I have map the tumor-normal pair exome data to genome using BWA and calling somatic mutation using Varcan. how to annotate somatic mutaion? just like classify the somatic mutation to missense_mutation or silent or frame_shift,etc.
thanks in advance.

[GenoMax]

COSMIC: http://varianttools.sourceforge.net/Annotation/COSMIC

SnpEff: http://snpeff.sourceforge.net/

[adamyao]

Online annotation tool VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/) capable of annotating millions of variants in minutes should be a good candidate to satisfy your expectation.

[Liam_Gallagher]

If you have the VCF file, you can also use wAnnovar: http://wannovar.usc.edu/

[m_two]

Ensembl VEP http://useast.ensembl.org/info/docs/...vep/index.html
will perform annotation for all transcripts, provides precomputed sift/polyphen scores, and indicates which variants are in dbSNP (mostly germline with MAFreq) and COSMIC (mostly somatic). It will also annotate regulatory features.

[m_two]

Another tool you may be interested in: https://github.com/ckandoth/vcf2maf

It uses snpEff to annotate all overlapping transcripts for each variant then filters the annotation to identify a single, best transcript isoform with the most severe effect and longest coding sequence.

The prioritization considers transcript biotypes and attempts to avoid pseudogenes and incomplete ORFs.