snpEFF not able to download GRCH38 ?

Question

[pinn]

HI Why snpEff not able to download GRCH38 ?

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

pinn@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)

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[Ram]

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!

[Ram]

Reopening question as user has provided feedback.

[Matteo Schiavinato]

What is your command? can you post it here?

[Ramana]

Sorry, its working with 38.86

[eliseujayro]

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

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

[Ram]

Did you try the solution posted below by genomax?

Answer 1

[GenoMax]

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

[Ramana]

I tried with 38.86 showing same error ?

[pinn]

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

[Ram]

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

Answer 2

[geocarvalho]

I had the same issue, just search for the version available and download it:

$ java -Xmx4g -jar snpEff.jar databases | grep GRCh38
OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
   526
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

GRCh38.99                                                       Homo_sapiens                                                                                                          https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.99.zip
GRCh38.p13.RefSeq                                               Human genome GRCh38 using RefSeq transcripts                                                                          https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p13.RefSeq.zip

$ java -Xmx4g -jar snpEff.jar download -c snpEff.config -v GRCh38.99