Package to retrive Cosmic data
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marco fabbri ▴ 320
@marco-fabbri-1657
Last seen 7.5 years ago
Italy

I have list of genes and I would like to retrieve informations about mutations and especially the frequency of each mutation related to specific disease. I would like to use COSMIC database since I work with somatic mutations. I have seen the cosmic 67 package but it looks pretty old.

Any package or solution to suggest?

Thank you

Marco

 

 

 

cosmic • 1.6k views
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@markusriester-9875
Last seen 21 months ago
United States

They changed their license recently (https://cancer.sanger.ac.uk/cosmic/license), so you need to register and accept their license. Once you have the VCF, you can use the VariantAnnotation package to retrieve Cosmic annotation for you somatic calls, e.g.:

    vcf <- readVcf("your.vcf", "hg19")   

    cosmicSeqStyle <- seqlevelsStyle(headerTabix(TabixFile(cosmic.vcf.file))$seqnames)

    vcfRenamedSL <- vcf
    if (!length(intersect(seqlevelsStyle(vcf), cosmicSeqStyle))) {
        seqlevelsStyle(vcfRenamedSL) <- cosmicSeqStyle[1]
    }

    # look-up the variants in COSMIC, specify all the info/fixed/geno fields you need. vcf needs to be bgzip'ed and tabix'ed

    cosmic.vcf <- readVcf(cosmic.vcf.file, genome="hg19",  
        ScanVcfParam(which = rowRanges(vcfRenamedSL),
            info="CNT",
            fixed="ALT",
            geno=NA
        )
    )

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sorry still not clear. Can I search for a list of genes? and filter for mutation known to be related to specific types of cancer?

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You complained that the COSMIC.67 package is old. The reason is the proprietary license, so the answer is no, there is no updated package. But you get the updated data after registration and the data contains all your requested information ( http://cancer.sanger.ac.uk/cosmic/download ). Take a look at the TSV file.

If you download the data as VCF, you can use VariantAnnotation for querying by genomic ranges as described in the COSMIC.67 vignette. 

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