small indel tool compatible with mapreads output from frag. library:

[JohnK]

Hi- looking for a small indel tool compatible with mapreads fragmented library mapping data. Notice that ABI has a small indel tool, but it appears to be for mate paired libraries. I know bfast has this ability, but I'd like to work off mapreads data right now. Thanks.

J

[Tuxido]

The small indel tool from solid also works for fragment libraries. But you then also need the SOLiD mapping tool to create the indel-evidence.pas file which is parsed by the indel tool.

[JohnK]

The small indel tool from solid also works for fragment libraries. But you then also need the SOLiD mapping tool to create the indel-evidence.pas file which is parsed by the indel tool.

Hey Tuxido,

Thank you for clarifying that for me- it will save much time and trouble.

[JohnK]

The small indel tool from solid also works for fragment libraries. But you then also need the SOLiD mapping tool to create the indel-evidence.pas file which is parsed by the indel tool.

v1.3 of the Small Indel tool doesn't happen to be encapsulated in the BioScope software does it? I have v1.1 and I'm not seeing any indel-finding-frag.pl script...