Problem with Jannovar and downloading hg19 db
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3.5 years ago
misterie ▴ 100

Hi,

I am trying to download RefSeq transcript database for the release hg19/GRCh37 and I have following problem:

the author of quick start tutorial wrote that after using a command:

$ java -jar jannovar-cli-0.27.jar download -d hg19/refseq

Jannovar should create data/hg19_refseq.ser file.

In my case after running that command, Jannovar creates ~/data/hg19/refseq directories with many files. I do not have hg19_refseq.ser that is necessary for downstream analysis.

Anyone had similar problem? How can I fix it?

Thank you in advance for your reply.

jannovar hg19 annotation • 894 views
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Hi, can you post the full output of jannovar download. I could then see whether the problem persists.

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