Annotating indels

[anjulka]

Hello,

I apologize for asking what may be a really silly basic question.

I identified cancer specific SNPs with GATK's Somatic Indel Detector, and then used the verbose output file to retrieve SNPs in coding regions with no or low counts in normal. These I then visually validated in IGV. However, my data is in a text file (well, excel file).

The indel calling part looks like:
Chrom Last Ref base Last event base Event
1 120612002 120612004 -GG
7 151927358 151927358 +A
X 66766356 66766377 -GGCGGCGGCGGCGGCGGCGGC
This is directly from the verbose output (sans header line as explanation). -GG means a deletion of GG. +A means an insertion of A at that location.

I've tried taking this into Oncotator, but that requires me to change the base pair numbers and how the event is labelled. Worse, all it does is say "p.P6fs" and "Frame Shift Del." I'm glad to know the amino acid, but I need to know if it creates a stop codon or what the base is changed to, etc.

I've seen people suggest SnpEff, and GATK recommends that too. However, SnpEff has deprecated their txt input. Plus, I have no idea how to get what I listed above into their recommended input format without what seems like a lot of manual work and possibly taking it into Oncotator first to get the strand.

Does anyone have any suggestions?

Thank you,
Rose

[Jane M]

You could try Annovar but you will have to change the input a little bit.
Jane

[anjulka]

It looks like Annovar also just labels things like p.G12fs.

Is what I'm thinking of just not done?

[Heisman]

What exactly do you mean by what a base is changed to when talking about indels?

[anjulka]

Say the original sequence at a point is TGT (Cys). An insertion occurs such that it's now TG[T]T. That would still be a Cysteine at that location, though it will likely mess up everything downstream. However, that might depend on what's downstream.
If the insertion instead is TG[A]T, that's an immediate stop codon.

So I would like an annotation program that tells me if the current codon is changed, if a stop codon is created downstream, and optimally whether the indel is deleterious overall (for example, from protein folding) if something like PPH2 or Mutation Assessor is incorporated.