SnpSift difficulty with Filter expression in Galaxy, which is fine on the command line version

Question: SnpSift difficulty with Filter expression in Galaxy, which is fine on the command line version

3.2 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

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 • 1.1k views

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modified 23 months ago • written 3.2 years ago by Guy Reeves • 1.0k

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.2 years ago by Guy Reeves • 1.0k

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

23 months ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k 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 COMMENT • link written 23 months ago by Guy Reeves • 1.0k

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