[ensembl-dev] Variation features named TMP_ESP_1_1693469 and similar???

[Anja Thormann]

Hi Jeremy,

rs# are assigned by dbSNP from where we import most of our variation data. But we have many more source from which we import data. One of these sources is the NHLBI GO Exome Sequencing Project (ESP). Not all variants from ESP have a rs#. In such a case we generate a temporary ID. For ESP data it is: TMP_ESP_CHROM_POS. The information is taken from a VCF file which is provided by ESP. Let me know if you need further clarifications.

Anja

On 7 Jan 2014, at 12:42, Jeremy Henty wrote:

> 
> Looking at the EnsEMBL variation data we display in Otterlace we
> noticed that not all of the features are named starting with "rs".
> For instance (in homo_sapiens_variation_73_37) there is a feature
> named rs1693469 with allele_string G/A and another named
> TMP_ESP_1_1693469 with allele_string TCC/- .  These two features both
> look like they have ID 1693469 yet they are different (because the
> allele_string is different).  Also, the EnsEMBL URL for rs1693469
> works, but the one for TMP_ESP_1_1693469 says not found.
> 
> We are not sure how best to handle this.  Should we display only
> features whose names begin with "rs"?  If we display TMP_ESP_1_1693469
> as well, is there a valid URL for it?
> 
> Jeremy Henty
> Anacode team
> Wellcome Trust Sanger Institute
> 
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