You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single series of nucleotides, and their complements, for each chromosome. What I don't see is two corresponding sequences. SNP data (e.g., SNPedia ) cites (if I understand it correctly) the SNP at the same site on each chromosome in the pair. I don't know how to determine my variation, since I see only one nucleotide at any given site, not the pair.
Pretty sure I'm missing something fundamental here. Thanks for any help navigating this jungle!