Finding In/Dels in Geneious

[nforce]

Hi,

I'm very new to analyzing sequencing data. After aligning my read to a reference genome in Geneious, how can I find segments of my genome that is deleted?

The Find SNP/Variations tool, is limited to regions with sufficient coverage. How can I precisely identify the range where there are deletions, since they have very low coverage.

Should I just use the Find Low coverage tool? Or is there a better way?

[GenoMax]

@nforce: When you are using a commercial program your best bet to get specific questions like this answered is to contact the tech support. Even though someone on the forum may be able to answer your question it may take a while for that person to come along. Since you are paying for the program may as well make use of tech support that comes with it.

[Matt Kearse]

Yes, you are best to contact Geneious support directly with any questions you have. But since I'm here I'll answer your question.

Geneious R9 includes mapper options called 'Find structural variants and deletions of any size' and 'Find large deletions up to ...'. Turn on either of those settings and in addition to mapping reads so that they span the deletions, it will create annotations for deleted regions with properties indicating the number of reads that support discovery of the deletion.