Strategy to detect deletions in the PE 300 reads

Question

[kspata]

Hi All,

I have PE 300 sequencing data of a circular plasmid sample. I want to detect deletions which occur at low frequency with deletion length in the range of 20bp to 50 bp. What tools can I use to detect these variants.

Samtools was not able to detect these deletion variants.

Thanks!!!

[WouterDeCoster]

I'd suggest pindel