What Do You Do With Indels Data?

Question

[User 2005]

I have a list of insertion and deletion from a whole genome sequence obtained by next generation sequencer,

chr, pos and sequence for each indels aligned to our reference genome.

I'm not familiar with this kind of study and the literature didn't give out anything. I was wondering where to start to analyze indels.

Any suggestion is always Welcome :)

Answer 1

[Sean Davis]

As a start, I'd suggest converting to VCF or a format understood by snpEff, Ensembl Variant Effect Predictor, Bioconductor VariantAnnotation package, or annovar. These programs are useful for determining the effects of small indels on coding genes.