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the dbsnp input in MuTect

jingmengjingmeng AustraliaMember

In MuTect2, the dbsnp is not a must input. If I do not provide dbsnp file when running MuTect2 on exome data, will MuTect2 treat all the sites as non-dbsnp sites, and use threshold of 2.2 in variant classification? If this is the case, how does it affect the sensitivity? Thanks for help.

Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @jingmeng,

    Apologies for the late reply, we failed to see your post come in.That's right, if you do not provide a dbsnp file the program will consider all sites as non-dbsnp and use the base LOD threshold. This means that variants will more easily be called as somatic. This may sound good but in practice it will mostly increase your false positive rate. Keep in mind that you can provide a COSMIC file to rescue any somatic variants that have been reported in dbsnp, which is a better way to ensure those sites are not penalized.

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