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.