Question: Is there any better method to find significant SNVs ?
gravatar for mangfu100
4.6 years ago by
Korea, Republic Of
mangfu100670 wrote:


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?

sequencing snp genome • 1.3k views
ADD COMMENTlink modified 4.6 years ago by poisonAlien2.7k • written 4.6 years ago by mangfu100670
gravatar for poisonAlien
4.6 years ago by
poisonAlien2.7k wrote:

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'

ADD COMMENTlink written 4.6 years ago by poisonAlien2.7k

+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).

ADD REPLYlink written 4.5 years ago by Charles Warden6.4k
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