Sequence Variation Detection For Prokaryotic Genomes

Question

[r.follador]

I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).

Which sequence variation detection software that uses paired-end information is recommended for such a task? I only tried LifeScope's LargeInDel-Analysis tool, but apparently it's not suited for bacterial genomes (I would have thought that this is the easiest case...).

Answer 1

[Raygozak]

after you have aligned your data, you may run your bam alignment through pindel which detects several types of SVs. As an alternative freebayes is for small SVs.

[r.follador]

thanks for your recommandation of pindel, I'll give it a try

[r.follador]

I did some extensive testing of Pindel using actual sequencing data and simulating some insertions and deletions of various sizes. Pindel seemed to be one of the software which had a high detection rate (very sensitive), but I found it almost impossible to distinguish between the true indels and false positives.