how to annotate somatic mutation？

zhaopeihua · 11-23-2013, 02:44 AM

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, 05:35 AM

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

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

adamyao · 11-24-2013, 05:22 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, 03:41 AM

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

m_two · 11-25-2013, 02:35 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, 01:46 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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11-23-2013, 02:44 AM	#1
zhaopeihua Member Location: china Join Date: Aug 2013 Posts: 18	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.

11-25-2013, 02:35 PM	#5
m_two Member Location: USA Join Date: Mar 2010 Posts: 49	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. Last edited by m_two; 11-25-2013 at 02:41 PM.

11-23-2013, 05:35 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,994	COSMIC: http://varianttools.sourceforge.net/Annotation/COSMIC SnpEff: http://snpeff.sourceforge.net/

11-24-2013, 05:22 PM	#3
adamyao Member Location: Taiwan Join Date: Feb 2011 Posts: 19	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.

11-25-2013, 03:41 AM	#4
Liam_Gallagher Member Location: Europe Join Date: Oct 2011 Posts: 18	If you have the VCF file, you can also use wAnnovar: http://wannovar.usc.edu/

11-26-2013, 01:46 PM	#6
m_two Member Location: USA Join Date: Mar 2010 Posts: 49	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.