Ensembl SNP

Load SNP data from a downloaded data file.

Types of data loaded

SNPs

How to download the data

First you will need the variation data from Ensembl, which are available via MySQL databases. Download the Ensembl file from their FTP site:

ftp://ftp.ensembl.org

Example:

ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_incl_consequences.vcf.gz

Download and unzip the file.

How to load the data into your mine

Add Ensembl snp to the list of datasources to be integrated

<source name="ensembl-snp" type="ensembl-snp">
  <property name="src.data.dir" location="/data/variation/ensembl/current" />
  <property name="ensembl-snp.includes" value="Homo_sapiens_incl_consequences.gvf" />
</source>

Run InterMine build

Run a build. The entry in project.xml will instruct the build process to load the GVF file you downloaded in the previous step into the database. For example, run this command in MINE_NAME/integrate:

$ ant -v -Dsource=ensembl-snp