How do i get the gap position from my .sam file?

[Petrichor]

Hi there!

For research purpose i need all the positions of gaps in my .sam file.
I took a look at them with Tablet, but i need the gaps as an extra file.

Is there an automatic way to do so, or do i have to do this manually?

Best regards,
Petrichor

[zgtmann]

Hello,

did you find some algorithm for extract gaps from .sam to bed? Could you post it here,please..

Thanks,

Petr.