Diverging results between STAR and BWA aligned inputs

[yasin-uzun]

Hi,

I am running squid with two types of inputs: 1) Samples aligned with STAR 2) Samples aligned with BWA

When using STAR output, I get less than 100 SV calls per sample. When I run with BWA output, I get several thousand SVs per sample. What is the source of this difference? Can you please give some information about this?