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-   -   how to annotate somatic mutation? (http://seqanswers.com/forums/showthread.php?t=36110)

zhaopeihua 11-23-2013 01:44 AM

how to annotate somatic mutation?
 
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 11-23-2013 04:35 AM

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

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

adamyao 11-24-2013 04:22 PM

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 11-25-2013 02:41 AM

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

m_two 11-25-2013 01:35 PM

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 11-26-2013 12:46 PM

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.


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