[Genome] 2 strong requests

[Brooke Rhead]

Hi Tim,

Thank you for the thoughtful suggestions.  Suggestion #1 is now on our 
list of topics to discuss at our next project meeting.

Concerning suggestion #2, our developers feel that changing the format 
of the 'observed' string might cause more confusion among our users than 
it is worth, especially since, as you pointed out, the information is 
already in the table.

Thanks again for sharing your ideas on improving the Browser.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Tim Hefferon wrote:
> 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
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