Mike,

There actually is not a way to get the deleted base(s) from the SAM alone, since SAM displays only the read and not the reference.


Thanks,
Kelly


On Wed Jun 8, at 4:58 PM, Mike Dufault wrote:

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
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