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Is there any better method to find significant SNVs ?

Hi.

I have worked with normal-tumor SNVs results by using VarScan2 and Mutect.

So I have total 500 candidate somatic nucleotide variants.

but problems is that there is so many snvs in my data. I need significant snvs which is related to cancer.

So I think that i have to search databases liek dbSNP or 1000genome.

so how to utilize above databases well? or Is there anything better method to find somatic variants in large sets?

genome sequencing snp
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updated by Ram Ram • written by mangfu100 mangfu100

1 answer

Go and paste your variants into oncotator.

The resulting maf has dbDSNP, COSMIC, TCGA, mutsig annotation data, which should be enough for you to begin with.

Also take a look at annovar if you want to 'search databases liek dbSNP or 1000genome'

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written by poisonAlien poisonAlien

+1 for ANNOVAR. I would recommend checking the ClinVar annotations. I've found that COSMIC includes a lot of variants, including ones with very high population frequencies (say >70%). In other words, ClinVar has a much smaller list of cancer variants than COSMIC (and the ClinVar cancer variants seem more likely to be rare variants).

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updated by Ram Ram • written by Charles Warden Charles Warden

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