I am trying to use the following expression in SnpSift " ( GEN.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.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.DP > 50)">
But when I use only " ( GEN.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