this question is conceptually similar to a previous one posted by Pierre Lindenbaum, but adapted to the SOLiD data. in fact, our group is planning to map SOLiD results to hg19 using the propietary software BioScope (free though till now). the problem is that although many of the groups we know that are working on NGS are sticked to hg18, none of them have been able to convince us not to use hg19 since we are focused on human variations and we always want to use the most up to date version of dbSNP (among other DBs). any thoughts on this matter?
by the way, is there anyone here using hg19 on BioScope? the default installation comes with hg18 files only, and surprisingly it doesn't seem to be straightforward to upgrade to hg19. there are other files apart from hg19.fa that anyone can get for instance from the UCSC genome browser, and we haven't been able to find anywhere else. of course LifeTech is "working on it", but I was wondering if any of you may have already solved this issue.