Limit of indel length with bwa

[nvteja]

Hi folks,

I am wondering whether there is a limit on maximum size of insertion/deletion inside a read that bwa checks when it is aligning? Like say there should not be a insertion or deletion of more than 10bp for 50bp reads? (for ex)

[nilshomer]

Check out the options in "bwa aln":

-o INT maximum number or fraction of gap opens [1]
-e INT maximum number of gap extensions, -1 for disabling long gaps [-1]