Linear versus affine gap cost

Question

[rtho]

I'm performing read alignment of whole exome seq data for tumor specimens, for variant detection. I'm having difficulty deciding whether to use linear or affine gap cost in my situation, can anyone give any pointers on factors that would favor one over the other? Thanks

[German.M.Demidov]

Affine gap cost is better since having a deletion of 20 letters should not be penalized as strict as having 20 deletions of 1 letter each. It is simply dependent on the probability of DNA machinery to make gaps/inserts of various sizes.

[rtho]

Thanks- that's useful