Blast InDels in CLC

Question

[chuck.barden3]

I am trying to use BLAST to analyze the "InDel" output from the tool in CLC called "InDels and Structural Variants." However, the BLAST tool is not available and I'm wondering if the InDel data set is in the wrong format. Anyone know how to change it to the right format in CLC? I was thinking "Convert from Tracks" would be the way to go but that is not an option either.

[Kevin Blighe]

Sorry Chuck - please contact Qiagen about this. It's their licensed program.

[Jonathanjacobs]

why was this thread closed?

• Chuck - the tool you're refering to creates a track file. If you are looking to export it - VCF format would likely be the best format. What is it you are trying to do with BLAST? align the insertions/deletions against one or more other references? if so - then you probably would want to convert your indel track to a consensus sequence first, then do the alignment with BLAST, the CLC aligner, muscle, clustal, etc.

[Kevin Blighe]

Re-opened. Thanks for stepping by, Jonathan, but, correct me if wrong, Qiagen's reps are not accustomed to drop in to Biostars (?). I gave advice to the user that I felt would allow them to receive help more quickly than had I not responded.

Thanks.