[Genome] 2 strong requests

[Tim Hefferon]

Hi,

I have two requests related to dbSNP tracks. Please consider:

1) Could you please include in the genome browser the ability to  
display SNP build 126 & 127 SNPs on genome build hg17, alongside  
build 125? (Perhaps a track showing all three at once in a separate  
track would also be a good idea.) By allowing access to only one  
version of SNPs, you are leaving out very important, updated SNP  
information that affects research. For example, when designing  
primers on hg17, I don't have access to current SNP data (126 & 127)  
that would affect primer choice. Yes, it is possible to do a lift- 
over of data from other builds, but that doesn't always work well -  
lots of errors are generated. I still work in hg17 - I don't know how  
much of the browsing community still does. It would be nice to be  
able to see current SNP data on hg17.

2) I don't know whether this is something you guys handle, or if it's  
in the realm of the dbSNP people at NCBI, but:  It is VERY nice to  
have indel polymorphism data available in the dbSNP track. However,  
when you download "all fields from selected table" to analyze SNP  
data, the genotype column does not indicate which polys are  
insertions and which are deletions. This info is included in  
surrounding columns, but it could be more efficiently indicated  
directly in the genotype (by placing the '-' before or after the '/',  
for example). Here's an example:

586	chr7	144935	144936	rs35756454	0	+	A	A	-/A	genomic	deletion	 
unknown	0	0	unknown	exact	1
586	chr7	146069	146069	rs34424236	0	+	-	-	-/A	genomic	insertion	 
unknown	0	0	unknown	between	1

It seems like using -/A to indicate insertion and A/- to indicate  
deletion would be an easily implemented and very useful switch:

586	chr7	144935	144936	rs35756454	0	+	A	A	A/-	genomic	deletion	 
unknown	0	0	unknown	exact	1
586	chr7	146069	146069	rs34424236	0	+	-	-	-/A	genomic	insertion	 
unknown	0	0	unknown	between	1

Thanks for considering,
Tim