Analysis pipeline

[Leo24]

Hi All,

I'm fairly new to sequencing and analysis of sequeincing data.

I've sequenced using the Ion Torrent Proton and I have a tumor and am comparing it to sequenced PBMC data from the same patient.

I'm looking for indels, snps and just trying to figure out what pathways may be affected by mutations in the cancer tumor.

What would be your workflow in general starting from the BAM file?
I'm using command line to analyse the data - what tools, or what would you use?

Thanks for any helpful suggestions!
Leo