Question: SnpEff variant annotation
2
gravatar for hov
14 days ago by
hov20
hov20 wrote:

Hello!

I am trying to annotate variants (Human genome) by SnpEff annotate variants (Galaxy Version 4.3+T.galaxy1) according to Galaxy tutorial ( https://galaxyproject.org/tutorials/var_dip/ ). How to fill out "Non-coding and regulatory annotation" field?

Thank you in advance!

snp variants galaxy snpeff • 73 views
ADD COMMENTlink modified 14 days ago by Jennifer Hillman Jackson25k • written 14 days ago by hov20
0
gravatar for Jennifer Hillman Jackson
14 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool was just updated and the tutorials do not reflect what changed yet (but will soon).

Right now, there are no native indexes on the server linked in. Use the "Genome Source >> Download on Demand" option. Available datasets can be reviewed at the help link (https://sourceforge.net/projects/snpeff/files/databases/v4_3/). The database names are in the archive names.

For example, if your input VFC is based on hg19 and has that database assigned, enter hg19 into the box for Snpff Genome Version Name.

I confirmed this by reviewing data at the help link and searching by database name.

Example: the hg19 archive is named like:

 snpEff_v4_3_hg19.zip

This can get a bit tricky but most can be worked out (for later, if/when doing your own analysis). For example, this one would be for galGal4 (VCF database assignment in Galaxy) and with Galgal4.75 entered into Snpff Genome Version Name:

snpEff_v4_3_Galgal4.75.zip

Whether or not there is an extra annotation that corresponds to "Non-coding and regulatory annotation" isn't a known before the tool is executed with this method, so it cannot be used as a filter. No filtering is used in the tutorial anyway (prior defaults used instead). This is likely temporary and will be resolved soon so that a built-in index can be used (especially those used in tutorials).

Once built-in indexes are available, clicking on the "Non-coding and regulatory annotation" box will list options to select/de-select (or something similar). The tutorial will update to reflect the proper usage/form pictures.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 14 days ago by Jennifer Hillman Jackson25k

Dear Jen, thank you for detailed answer! I followed your recommendations, but SnpEff eff generates fatal error (see below). How can I overcome it? Thanks!

Fatal error: Exit code 255 (Error) Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/019/744/19744333/_job_tmp -Xmx7g -Xms256m java.lang.RuntimeException: java.lang.RuntimeException: Cannot create directory '/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/data/hg19' at org.snpeff.util.Download.unzip(Download.java:296) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:33) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72) at org.snpeff.SnpEff.run(SnpEff.java:1221) at org.snpeff.SnpEff.loadDb(SnpEff.java:515) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) Caused by: java.lang.RuntimeException: Cannot create directory '/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/data/hg19' at org.snpeff.util.Download.unzip(Download.java:264) ... 9 more java.lang.RuntimeException: Genome download failed! at org.snpeff.SnpEff.loadDb(SnpEff.java:516) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162)

ADD REPLYlink modified 12 days ago • written 12 days ago by hov20
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