Hello everybody, I am dealing with a dataset of cancer tumours sequenced on hiseq. 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?
2) Is the judgement criteria i.e. "KEEP" or "REJECT" an absolute criteria? 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? There is a lot of ambiguity surrounding this, and I would love to hear the communities thoughts on this subject.
Thanks a lot for your 2 cents!
1) How good is mutect at calling variants, when there is no matched normal supplied?
2) Is the judgement criteria i.e. "KEEP" or "REJECT" an absolute criteria? 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? There is a lot of ambiguity surrounding this, and I would love to hear the communities thoughts on this subject.
Thanks a lot for your 2 cents!
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