seqmule-download downloads reference genomes, index files, capture region definitions and other databases.


    seqmule download <options>


This command downloads specific database files used in analysis, including but not limited to, reference genomes, index for reference, dbSNP database, 1000G indel database, capture region definitions from various manufacturers.


    --down,-d               comma-delimited list of databases and BED files by capture kit manufacturer. See details.
    --downdir <dir>         custom download folder. NOT recommended if you want to use default databases.
    -v,--verbose            verbose output. Default: disabled
    -h,--help                       help
    --noclean                       do not clean temporary files
    --debug                 debug mode


    #download all hg19 databases/BEDs to default location (under installation directory)
    seqmule download -down hg19all

    #same as above, but saved at custom location
    seqmule download -down hg19all -downdir /home/user/database


  • --down

    The following list gives possible options and their corresponding databases. You can use 'hg19all','hg18all','all' to download all databases corresponding to a specific genome build or all databases. Default location for databases is 'installation_directory/database/'.