I have recently run into the issue of finding relatively recent databases and papers which align to the old reference assembly (HG 19 / GRhC37).
I understand that it is non-trivial to change alignments, but this assembly was last patched in 2013. For novel projects, especially, it should be trivial to use the latest assembly.
Can someone please help me understand why new projects are using the older assembly?
3 answers
i wouldn't hold your breath
Pubmed central full-text searches e.g. https://www.ncbi.nlm.nih.gov/pmc/?term=((%222015%22%5BElectronic+Publication+Date%5D+%3A+%222015%22%5BElectronic+Publication+Date%5D))+AND+grch37%5BText+Word%5D
hg38 hg19 grch37 grch38
2019 279 1050 511 383
2018 728 3354 1550 997
2017 567 3730 1590 764
2016 299 3413 1441 465
2015 105 2977 1224 228
some reproducible code to plot cumulative mentions
library(ggplot2)
library(lubridate)
library(tidyr)
library(dplyr)
freezes<-read.table("freezes.txt",sep="\t",header = TRUE)
freezes %>%
gather(term, mentions, -year) %>%
group_by(term) %>%
arrange(year) %>%
mutate(cmentions = cumsum(mentions)) %>%
mutate(year=ifelse(year==2019,2019+(yday(Sys.Date())/365),year+1)) %>%
ungroup() %>%
mutate(term=factor(term,levels=c("hg19","grch37","grch38","hg38"))) ->
freeze_plotable
ggplot(freeze_plotable,aes(year,cmentions))+geom_smooth(aes(color=term))

I'll go on a limb here and say that there is no clear benefit of switching from hg19 to hg38 for most purposes.
So hg19 will become obsolete same time as hg38, when using graph-based genome reference will become feasible.
I think some databases are only for hg19. You could lift them over, but I would guess some things will be different for a direct alignment versus a liftOver annotation. For example, some variant frequencies should be affected by the genome build and/or pre-processing steps.
I think having multiple genome options is good (and, if you are looking at certain genes, like HLA genes, using a custom reference may be preferable to the main genome build).
However, if you are mostly comparing to previous samples (say, 90% of your data is already aligned to hg19), I think many analyses will be OK for adding new samples to the previous alignment. However, if you encounter a strange result, seeing if updating the reference (or other steps) may be worth checking (if nothing else, it could give you confidence the issue is less likely to be due to the genome reference).
I think the genome build is a bigger issue for other organisms with fewer genome revisions. Some programs like i-cisTarget provide analysis for the older mouse build (mm9) as well (and I think there are some situations where that program can be useful). However, I'm having a hard time thinking of an example of a resource where the reference sequence / curation is at an even earlier stage.
Log in to answer this question.
GRCh37, IMO, is the equivalent of IBM mainframe computers, especially with clinical informatics. It is a sequence that works well enough to not be a pain to most research folks. IIRC, even NCBI/dbSNP only made the switch relatively recently. I think GRCh37 is going to be around for a few more years at least. It will take major tools deprecating support for GRCh37 for the forced switch process to start.