First post here, complete newbie. I'm not sure if this is the relevant place to ask this, so please excuse me if I'm wrong.
I have done WGS at Dante Labs and imported the BAM (100GB) file in sequencing.com. The import in Promethease is still pending. I would like to be able to explore "my own" configuration of all known SNPs up to date. For example if I'm reading an article that mentiones rs10994415, rs1006737 and other SNPs, I expect to copy-paste it in sequencing.com selecting the "Variant" column and to see my genotype. However some SNPs are present, but others aren't.
What am I missing? Initially I had a .VCF.GZ file which was supposed to be the "difference" between my genes with the reference genome. My assumption was that the missing SNPs were missing, because they were the same as the reference genome and hence not shown in sequencing/promethease. That's why I requested the BAM file, expecting it to be "my own differences aligned with the reference genome", so all possible SNPs would be included.
Please excuse my lack of knowledge. I'm trying to deal with something out of my expertise domain and I'm unable to understand what's going on for weeks.