structural variants:CNVs and deletions

[kinu]

Hi all,

I have Illumina paired end reads for pooled data from cows. I am looking for large structural variants. what should I start with specially for the pooled data.

The reads length is 100bp with insert 150bp.

Looking forward for suggestions and literature or Tools that can used.
I am aware of large list of tools available for this, but the complication is the pooled data.


Thank s in advance
Kinu/