Loading Genomics DB - GenomicsDB/GenomicsSampleAPIs GitHub Wiki

This section assumes that you have an existing csv file which has associated data in MetaDB, as well as vid_map and a callset_map. If you do not have this and would like to produce one, you can run the vcf2tile.py or maf2tile.py as appropriate without -l.

To load the data:

  1. Create a GenomicsDB loader config as specified here in the GemoicsDB wiki.

  2. Assuming GenomicsDB/bin is in your path run:

    vcf2tiledb /path/to/loader/config

    or if you have mpi partitions:

    mpirun -n <num_partitions> [-hostfile <hostfile>] ./bin/vcf2tiledb /path/to/loader/config

    Note: mpi options can be specified in load_to_tile.cfg in option1.

  3. Sanity Check: provides more information for validating that the variant data was correctly loaded into the TileDB array.

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