Turn off indel calling?

[W. Evan Johnson]

Can I turn off indel calling in the newest GNUMAP?

[changjin hong]

The Indel means insertion or deletion in an alignment transcript? Can
you give me an simple example of how you want to turn off indel calling?

[Evan Johnson]

Changjin,

You are correct about the definition of indels. The newest GNUMAP-SNP
can call indels, but I don't want to call them in some of my projects,
just wanted to turn this off.

Evan

[Nathan Clement]

The indel calling only prints extra information at each position in the genome. Are you simply asking to remove the stuff at the end of each line in the gmp file?

[W. Evan Johnson]

Yes, but previously the pair-HMM did not allow gaps. Can I add a flag to go back to this?