Variant Calling - Ion Torrent

Question

[AndreaSibi]

Hello to everyone,

It is probably a stupid question but starting now with the bioinformatics domain, I would like to ask.

I already performed some variant calling experiments on Illumina data, by starting from .fastq files and going through the variant calling phase.

Now, for the first time, I have a dataset of Ion Torrent data..here I don't have fastq files but rather I have .bam files (aligned files).

The question is..can i go directly through the variant calling step? Or do I need to transform these .bam files into .fastq file and perform the quality control and again the alignment on these ones? (in this second case, i want to ask you if there is a loss of information by passing from .bam files to the .fastq)

Thank you for the attention.

[newbio17]

Ion Torrent workflow is a bit unconventional compared to what you're probably used to with Illumina data. When I had to deal with such data in the past, I found some help in a previous Biostars post here, specifically the part where it talks about how .bam files generated from Ion Torrent stores additional information which TVC (Torrent Variant Caller) uses to perform variant calling.