This data loader takes the data available at ftp://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/ (files at qtl_as), and it stores the contents into the Elasticsearch database instance used by BLUEPRINT WP10 data portal.
It also needs the correspondence between methylation probe ids and their positions. It can be generated using gen450kManifest.bash script, running next command line:
bash gen450kManifest.bash meth_450K_pos.txt
This Perl script depends on the dependencies listed in cpanfile, which can be installed using cpanm using a sentence like:
cpanm --installdeps .
- The data loader fetches a dbSNP copy in VCF format, as well as its index, based on the setting in the WP10 data model. See blueprint-setup-wp10_template.ini for the settings.
- The data loader depends on vcftools, which must be found through
PATH. - It also depends on
tabix, available in HTSlib / Samtools package.