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General Discussion
Annemarie Eckes
2016-11-28
2016-11-28

  • Annemarie Eckes

    Annemarie Eckes - 2016-11-28

    After doing
    $ java -jar snpEff.jar databases
    I found that there was a database available for brassica napus:
    http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_brassica.napus.zip
    But wasn't able to download it.
    I have tried to find the file here, to download manually, but had to go back to v.4_1 to find the database. Is v.4_3_brassica.napus actually available??

    Thanks in advance!

     

  • David Yarmosh

    David Yarmosh - 2017-08-23

    I found plenty of H37Rv in the config file, but I'm not sure which value t use to download with the java -jar snpEff.jar download function.

    I also tried using the default example so i could get a feel for it, but something didn't work.

    $ java -jar snpEff.jar download GRCh38.76
    java.lang.RuntimeException: Property: 'GRCh38.76.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:106)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:680)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:648)
    at org.snpeff.snpEffect.Config.init(Config.java:479)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)

     

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