"ArithmeticException" in VariantFiltration and "Invalid JEXL expression detected" in SelectVariants

zugzug

Hi,

I have been trying get variants out of a VCF file where the Allele Frequency (AF) is greater than 4%. I have tried both VariantFiltration and SelectVariants but I get different errors with each. Here is my call for SelectVariants:

java -Xmx4g -jar ~/tools/bin/GenomeAnalysisTK.jar -R /home/genome/human_g1k_v37.truseq_mask.fasta -T SelectVariants -o S05-16209-1C_S4_L001_R1_001.30.10.sorted.3perc.vcf --variant S05-16209-1C_S4_L001_R1_001.30.10.sorted.vcf -select "AF > 0.04" -sn "S05-16209-1C_S4_L001_R1_001"

The error is:

MESSAGE: Invalid command line: Invalid JEXL expression detected for select-0 with message ![0,9]: 'AF > 0.04;' > error

For VariantFiltration the call is:

java -Xmx4g -jar ~/tools/bin/GenomeAnalysisTK.jar -R /home/genome/human_g1k_v37.truseq_mask.fasta -T VariantFiltration -o S05-16209-1C_S4_L001_R1_001.30.10.sorted.3perc.vcf --variant S05-16209-1C_S4_L001_R1_001.30.10.sorted.vcf --filterExpression 'AF > 0.040' --filterName "3perc"

The error is:

java.lang.ArithmeticException: Double coercion: java.util.ArrayList:([0.010, 0.010])
at org.apache.commons.jexl2.JexlArithmetic.toDouble(JexlArithmetic.java:1023)
at org.apache.commons.jexl2.JexlArithmetic.compare(JexlArithmetic.java:699)
at org.apache.commons.jexl2.JexlArithmetic.greaterThan(JexlArithmetic.java:790)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:796)
at org.apache.commons.jexl2.parser.ASTGTNode.jjtAccept(ASTGTNode.java:18)
at org.apache.commons.jexl2.Interpreter.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at org.broadinstitute.sting.utils.variantcontext.JEXLMap.evaluateExpression(VariantJEXLContext.java:267)
at org.broadinstitute.sting.utils.variantcontext.JEXLMap.get(VariantJEXLContext.java:233)
at org.broadinstitute.sting.utils.variantcontext.JEXLMap.get(VariantJEXLContext.java:118)
at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.match(VariantContextUtils.java:293)
at org.broadinstitute.sting.gatk.walkers.filters.VariantFiltration.filter(VariantFiltration.java:331)
at org.broadinstitute.sting.gatk.walkers.filters.VariantFiltration.map(VariantFiltration.java:270)
at org.broadinstitute.sting.gatk.walkers.filters.VariantFiltration.map(VariantFiltration.java:80)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

For both I have tried variations of double quotes and different sigfigs. Also, it works when I select on parameters other than AF.

Am I missing something?

ebanks

Your problem is that for multi-allelic variants the AF is not a double - it's a list of doubles. So the expression "AF > 0.04" is invalid in those cases.

Geraldine_VdAuwera

Have you checked that all your variants have the AF annotation? If it's missing in some of the variants in your VCF, the evaluation will fail -- and the error message tends to be unhelpful.

zugzug

Thank you for the prompt response!

I just performed the following command and all I got back was the header: grep -v "AF=" ../MiSeq_vs_Torrent-GATK/MiSeq/4plex/S05-16209-1C_S4_L001_R1_001.30.10.sorted.vcf | less

Any other ideas?

Geraldine_VdAuwera

If I remember correctly you should be able to extract variants that have the AF annotation with this command:

java -jar GenomeAnalysisTK.jar -T SelectVariants -R ref.fasta --variant my.vcf -o withAF.vcf -select 'vc.hasAttribute("AF")'

Then you can run your original command on the output subsetted VCF.

I'll see if others on the team can chime in -- I don't use JEXL much myself so there may be a more efficient way to do this -- but this should at least give you a way forward for now.

For more detail on using JEXL expressions, see http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk

zugzug

I'll give that a shot in a bit, but there weren't any lines missing AF. I have also been through the JEXL page and didn't find anything that I did incorrectly. Though I certainly may have missed it... :)

Thanks for your help!

zugzug

Let clarify that the grep command I did before means that ALL variants had the AF annotation.

Geraldine_VdAuwera

Ah, thanks for the clarification, that's not what I had understood -- then I'm not sure what your problem might be, since your expression is pretty simple and seems correctly written.

The error message suggests a type error, so you could try checking how the values are written in your VCF. If any of your AF fields are written as anything other than doubles (maybe a one is a 0 instead of 0.0, causing it to be read in as an integer), that would cause the evaluation against your query to fail. Maybe try to run on a few short intervals, and see if you can isolate some records on which your query works and some on which it doesn't, then compare what is different between them.

Good luck!

zugzug

Yes, the list of AF's was, in fact, the problem. Two questions: (1) What do you suggest is the best approach for handling these situations; and (2) Do you all plan to handle this situation within the tools in the near future?

ebanks

If you want to use the AF filter with JEXL expressions then you'll need to skip multi-allelic sites. Unfortunately, it isn't something we plan on addressing within the JEXL code anytime soon.

zugzug

Ok, by "skip" you mean the argument --restrictAlleles BIALLELIC in SelectVariants. Thanks again!