Question: snpEFF not able to download GRCH38 ?
0
gravatar for pinn
3.0 years ago by
pinn70
pinn70 wrote:

HI Why snpEff not able to download GRCH38 ?

Always its showing error, But its work well with GRCH37 reference. Thanks for your comments.

likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ 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:681)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    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)

T

annotation genome • 3.1k views
ADD COMMENTlink modified 3.0 years ago by GenoMax94k • written 3.0 years ago by pinn70
1

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by _r_am32k

Reopening question as user has provided feedback.

ADD REPLYlink written 2.7 years ago by _r_am32k

What is your command? can you post it here?

ADD REPLYlink written 3.0 years ago by Macspider3.3k

Sorry, its working with 38.86

ADD REPLYlink written 3.0 years ago by Ramana0

The same thing happened to me. The command is: java -jar snpEff.jar download GRCh38.76

-> http://snpeff.sourceforge.net/download.html

ADD REPLYlink written 2.6 years ago by eliseujayro0

Did you try the solution posted below by genomax?

ADD REPLYlink written 2.6 years ago by _r_am32k
3
gravatar for GenoMax
3.0 years ago by
GenoMax94k
United States
GenoMax94k wrote:

Try 38.86. That seems to be the latest GRCh38 as of now.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by GenoMax94k

I tried with 38.86 showing same error ?

ADD REPLYlink written 3.0 years ago by Ramana0

Sorry for late reply, I'm able to download it.

ADD REPLYlink written 2.7 years ago by pinn70
2

Please accept genomax's answer if it worked for you.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by _r_am32k
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