Variant calling on sample from both Illumina and Proton technology

Question

[vmicrobio]

Hi all!

I'm working with microorganisms and looking for variants (somatic). It has been said to me that in Proton outputs (bam), flowspace is used for statistical evaluation of false negative and false positive, and excluding floworder (by doing fastq) will lead to noisy results for variant caller. I would like to compare samples sequenced from different technologies (Proton and Illumina) however I haven't a control present in each technology.

Is it ok to call variant excluding floworder for Proton data or not? What pipeline should I use : something with bam from Proton and realign fastq from Illumina on the other side?

Does anybody has an experience with comparison of 2 technologies on variants? or suggestions?

Thank you for your feedback!