burden test/SKAT on exome study without control

Question

[zizigolu]

hi,

I read that when we have no control in exome-seq, we should use something like 1000 genome as control and performing statistical test. if prioritization of sequence variants by tools like TAPER, PhenIX, Exomiser, FAVR, VAAST, etc, means the same and compensate for lack of controls??

thank you

[Brice Sarver]

No control in what context? And what do you mean by control? For exome sequencing of clinical samples?

[zizigolu]

sorry,

this is detail of my experiment please help me

We have access to exome-sequencing data from an independent set of leukemic samples from a mouse model with an induced oncogene. However, these samples do not have an associated paired (normal) control. I should come up with a pipeline for how to try to identify mutations in the absence of such paired/normal controls

thank you in advance

[Ram]

I'm adding the relevant part of this reply to the question. In the future, if you forget to add a detail in the question, I'd recommend adding it to the question in addition to clarifying it in the reply you give to the person that asks for that clarification.

[zizigolu]

thank you Ram :) :) :)

[zizigolu]

I think the problem is lack of control in clinical samples