Question: SnpSift difficulty with Filter expression in Galaxy, which is fine on the command line version
1
gravatar for Guy Reeves
2.4 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI

I am trying to use the following expression in SnpSift  " ( GEN[0].DP > 50) "   which should filter the first SNPs based on wether or not the first sample (sample 0)  has a depth of more than 50.  

 cat Galaxy99.vcf | java -jar SnpSift.jar filter " ( GEN[0].DP > 50) " > filtered.vcf

When I try this on a comand line version of the SnpSift this expression works fine and I get what I want .  The following line is added to the output  vcf giving version details.##FILTER=<ID=SnpSift,Description="SnpSift 4.1i (build 2015-08-14), by Pablo Cingolani, Expression used: ( GEN[0].DP > 50)">

But when I use only  " ( GEN[0].DP > 50) "  on usegalaxy.org with the same input file it get a red error.

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
line 2:2 no viable alternative at character '"'
line 2:22 no viable alternative at character '"'
Exception in thread "main" java.lang.RuntimeException: Error: Genotype field 'DP' not ava

Does anybody have any ideas what is wrong?  Thanks Guy

 

 

 

 

 

snpeff snpsift vcf filter • 758 views
ADD COMMENTlink modified 13 months ago • written 2.4 years ago by Guy Reeves1.0k
1
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi Guy,

This is at http://usegalaxy.org, correct? Would you be able to share the history with galaxy-bugs@lists.galaxyproject.org? I'd like to review the exact inputs, tool version, and tool options and do some testing. Please put a link to this biostar question in the email.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson23k

Hi Jen 

Yes it is http://usegalaxy.org.  Here is the history-I will not delete it.

 https://usegalaxy.org/u/guy1/h/errorreportsnpsift 

I have submitted and error report with a link. This is not just a problem using a specific variable, I suspect it is more widespread.

Thanks again Guy

ADD REPLYlink written 2.4 years ago by Guy Reeves1.0k

I agree, the default is just a good simple example. Thanks for sending in the history. Under more review. Will post back soon. Jen

ADD REPLYlink written 2.4 years ago by Jennifer Hillman Jackson23k

The correct expression syntax is a simplified version, no quotes, no genotype field specified. Example: ( DP > 50 )

The tool VCFfilter can also be used for the same operation.

Hope this helps all with usage! Jen, Galaxy team

ADD REPLYlink written 2.4 years ago by Jennifer Hillman Jackson23k
0
gravatar for Guy Reeves
13 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

This whole issue was due to an old version being installed on usegalaxy.org which did not the documentation which was current and for the latest version. When i installed from the toolshed a more updated version on my galaxy instance I had no problems.

ADD COMMENTlink written 13 months ago by Guy Reeves1.0k
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