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Mutect Analysis without a paired tumour normal & Analysis Criteria

Hello everybody, I am dealing with a dataset of cancer tumours sequenced on illumina hiseq 1000. I do not have a matched normal, and I have used Mutect to call somatic variants. I have the following doubts:

1) How good is mutect at calling variants, when there is no matched normal supplied? Should it even be used for this purpose?

2) On what basis is this criteria decided? Will i loose out on a lot of quality variants, if i discount all the variants marked as "REJECT" by mutect, and proceed ahead with only variants marked as "KEEP" in my downstream analysis? Alternately, will keeping all the "REJECTS" (which pass a certain mutant allele depth criteria) increase my false positives? Is the judgement criteria i.e. "KEEP" or "REJECT" an absolute criteria & to be strictly followed, or are there other parameters which I should look at as well? I am specifically asking in context of an analysis where there is no matched tumor normal. I would love to hear the communities thoughts on this subject.

Thanks a lot for your 2 cents!


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