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Old 11-23-2013, 01:44 AM   #1
zhaopeihua
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Default 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.
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Old 11-23-2013, 04:35 AM   #2
GenoMax
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COSMIC: http://varianttools.sourceforge.net/Annotation/COSMIC

SnpEff: http://snpeff.sourceforge.net/
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Old 11-24-2013, 04:22 PM   #3
adamyao
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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.
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Old 11-25-2013, 02:41 AM   #4
Liam_Gallagher
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If you have the VCF file, you can also use wAnnovar: http://wannovar.usc.edu/
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Old 11-25-2013, 01:35 PM   #5
m_two
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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 01:41 PM.
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Old 11-26-2013, 12:46 PM   #6
m_two
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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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