Question: snpEFF not able to download GRCH38 ?
0
gravatar for pinninti1991reddy
14 months ago by
pinninti1991reddy30 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 • 1.2k views
ADD COMMENTlink modified 14 months ago by genomax65k • written 14 months ago by pinninti1991reddy30
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 12 months ago • written 12 months ago by RamRS21k

Reopening question as user has provided feedback.

ADD REPLYlink written 11 months ago by RamRS21k

What is your command? can you post it here?

ADD REPLYlink written 14 months ago by Macspider2.8k

Sorry, its working with 38.86

ADD REPLYlink written 14 months 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 10 months ago by eliseujayro0

Did you try the solution posted below by genomax?

ADD REPLYlink written 10 months ago by RamRS21k
3
gravatar for genomax
14 months ago by
genomax65k
United States
genomax65k wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by genomax65k

I tried with 38.86 showing same error ?

ADD REPLYlink written 14 months ago by Ramana0

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

ADD REPLYlink written 11 months ago by pinninti1991reddy30
2

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

ADD REPLYlink modified 11 months ago • written 11 months ago by RamRS21k
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