Exome seq analysis for Ion S5 sample

Question

[Kritika]

Hello All Recently I got some new project from Ion S5 sample (human sample) I want to try open source software with this data (starting from QC to Annotation) I dont want to use Tmap or Torretsuite So can any only help me knowing tools like FASTQC , GATK and samtools which can be used for Ion S5 samples.

Thanks

[h.mon]

Both TMAP and TorrentSuite are open source, more specifically, GNU GPL 2.0. If your restriction is using only open sorce, excluding them does not apply.