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What should I do if I don't have cosmic.vcf and dbsnp.vcf when using muTect?

Hi @kcibul‌ ,
I have some quires about muTect when using it.
For mammals such as human, there are dbSNP and COSMIC SNP database. But in plant, there aren't such database, at least no COSMIC database. I know there is no "tumor" in plant. But my data is similar to data from tumor.
So what I want to know are: 1) What are dbSNP and COSMIC SNPs used for in muTect? 2) Can I still use muTect under the situation I mentioned?
Best,
Zeamxie

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @zeamxie,

    dbSNP is used to reject candidate mutations that are most probably germline because they have been observed in other people. Because the level of validation of submissions to dbSNP is low, we are not confident that things being flagged as germline or somatic are trustworthy.

    In contrast, COSMIC is a more highly validated resource, so it is used essentially as a whitelist to "rescue" candidate mutations that would otherwise be rejected for being in the panel of normals and/or dbSNP. We expect that anything that is really somatic that is flagged as such in dbSNP will also be in COSMIC, so we can rely on COSMIC to rescue those sites.

    I can't comment on whether MuTect is appropriate for your data because I don't have enough information about what youhave and what you want to do. If you describe your experiment in more detail perhaps then I can help.

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