I'm pretty new to genome analysis, so apologies if this is a silly question. I have a 52x coverage personal genome in BAM format which I have converted to FASTA using the hs37d5 reference sequence using SAMtools etc. as detailed here. I can also download annotations mapped against the reference sequence such as gene tracks (e.g. GENCODE GTF files).
Say that I now want to use my personal genome as a reference. I assume that the locations on my new FASTA file won't correspond exactly to locations on the reference sequence: some introns will be of different lengths to the reference, etc. So what command-line magic to I need to do to convert the GTF (or other annotation) file so that it maps to my personal genome, rather than the reference? I assume this will involve throwing away some annotations (where the personal genome may have deletions), and there will probably be areas where the personal genome has extra duplicated genes, but I guess it will be difficult to detect these.
As it happens, I'd also like to display Alu repeats on my personal genome: these will presumably differ quite a lot from the reference. So are there any tools I can use to create an annotation track for repeated sequences against a personal genome sequence? Can I BLAST along my personal FASTA file and create an annotation track out of that?