Difference between Whole Exome Sequencing Pipeline for IonTorrent and Illumina?

Hello Everyone,

I have a Whole Exome Sequence Pipeline for Paired End. I wanted to ask that is there any difference between pipeline for the data coming from IonTorrent and Illumina. Can I use the Fastq file of IonTorrent in the Illumina pipeline or do I have to change any parameters/tool in the pipeline for different data.

Hope this is understandable.
Thank you 🙂