Question: dbSNP build in ENSEMBL biomaRt?
0
gravatar for 09meh
8 months ago by
09meh0
09meh0 wrote:

I'm wondering how to determine what dbSNP build (i.e. 150 or 151) the variation annotations are based on. For example, I can find that for GRCh37, this is based on Ensembl Variation 94. The SNP attributes state that the source is dbSNP but not what build:

grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice")
listMarts(grch37)
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
2     ENSEMBL_MART_SNP  Ensembl Variation 94
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94
variation = useMart(biomart="ENSEMBL_MART_SNP", host="grch37.ensembl.org", path="/biomart/martservice")
listDatasets(variation)[12,]
        dataset
12 hsapiens_snp
                                                                      description
12 Human Short Variants (SNPs and indels excluding flagged variants) (GRCh37.p13)
      version
12 GRCh37.p13

snps = useMart(biomart="ENSEMBL_MART_SNP", host="grch37.ensembl.org", path="/biomart/martservice",dataset="hsapiens_snp")

getBM(attributes=c('refsnp_id','refsnp_source',"refsnp_source_description" ,'chr_name','chrom_start','chrom_end','minor_allele','minor_allele_freq','minor_allele_count','consequence_allele_string'), filters = 'snp_filter', values ="rs123", mart = snps)

  refsnp_id refsnp_source
    1     rs123         dbSNP
                                     refsnp_source_description chr_name chrom_start
    1 Variants (including SNPs and indels) imported from dbSNP        7    24966446
      chrom_end minor_allele minor_allele_freq minor_allele_count
    1  24966446            C          0.292133               1463
      consequence_allele_string
    1                       C/A

1) Is this information available programtically through biomaRt? 2) If not, is http://grch37.ensembl.org/info/genome/variation/species/sources_documentation.html the best place to find this information? It unfortunately looks like the documentation link on this page (http://grch37.ensembl.org/info/genome/variation/prediction/sources_phenotype_documentation.html) is currently broken.

dbsnp biomart ensembl • 375 views
ADD COMMENTlink modified 8 months ago by Emily_Ensembl18k • written 8 months ago by 09meh0

An additional source of confusion: searching for individual SNPs on the GRCh37 ENSEMBL website (i.e. http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=7:24965946-24966946;v=rs123;vdb=variation;vf=119) gives information from dbSNP build 150: "Original source: Variants (including SNPs and indels) imported from dbSNP (release 150)" despite "Ensembl GRCh37 release 94" stated at the bottom of the page. So perhaps we can't assume that http://grch37.ensembl.org/info/genome/variation/species/sources_documentation.html is true for all Ensembl 94/GRCh37 data?

ADD REPLYlink modified 8 months ago • written 8 months ago by 09meh0

Tagging: Emily_Ensembl

ADD REPLYlink written 8 months ago by genomax70k
2
gravatar for Emily_Ensembl
8 months ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

GRCh37 is on dbSNP 150. In our release next month it will be updated to 151.

ADD COMMENTlink written 8 months ago by Emily_Ensembl18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1096 users visited in the last hour