Hi All,

 

Does anyone know if there is a way to get the deleted base information that corresponds to the "Extract indels from SAM" output?

 

The output from this tool includes the bases for insertions or "-" for deletions. I want to get the actual bases instead of the "-".

 

I assume there is a way to use the SAM file to extract the information, but if someone already has a nifty way to do it, that would be great.

 

Thanks,

Mike