VCF files

Load SNP data from a VCF file

Types of data loaded

SNPs

How to download the data

First you will need a VCF file, here is an example:

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

How to load the data into your mine

Add vcf to the list of datasources to be integrated

<source name="my-data-source" type="vcf">
  <property name="src.data.dir" location="/data/variation/current" />
  <property name="vcf.includes" value="*.vcf" />
  <property name="vcf.vcfTaxonId" value="9606" />
  <property name="vcf.vcfDataSetTitle" value="Ensembl SNP data set" />
  <property name="vcf.vcfDataSourceName" value="Ensembl" />
</source>

Run InterMine build

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

$ ant -v -Dsource=my-data-source