Hello Everyone,

I'm new to GATK pipeline. I installed GATK3.8 and filtering variants for my .vcf file.

However it throws error. Details of error is given below. Can someone help in this regard.

Below is the command to filter the variant: 

java -Xmx10G -jar /home/ngs/NGS_Tools/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar -T VariantFiltration -R /home/ngs/NGS_Tools/GATK_Resource_Bundle/hg19.fasta -V raw_variants_recal.vcf --clusterWindowSize 10 --clusterSize 3 --filterExpression "MQ >= 10 && ((MQ / (1.0 * DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" --filterExpression "DP < 10" --filterName "LowCoverage" --filterExpression "QUAL < 30.0 " --filterName "VeryLowQual" --filterExpression "QUAL > 30.0 && QUAL < 40.0" --filterName "LowQual" --filterExpression "QD < 1.5" --filterName "LowQD" -o HC_filtered_final.vcf

INFO 16:09:38,632 HelpFormatter - Date/Time: 2020/06/25 16:09:38
INFO 16:09:38,632 HelpFormatter - ------------------------------------------------------------------------------------
INFO 16:09:38,632 HelpFormatter - ------------------------------------------------------------------------------------
INFO 16:09:38,649 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/ngs/NGS_Tools/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so
INFO 16:09:38,664 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 16:09:38,664 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 16:09:38,665 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:09:38,765 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 16:09:38,879 GenomeAnalysisEngine - Preparing for traversal
INFO 16:09:38,883 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:09:38,883 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:09:38,883 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:09:38,883 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
##### ERROR --
##### ERROR stack trace
java.lang.NumberFormatException: For input string: "30.94"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.parseLong(Long.java:631)
at org.apache.commons.jexl2.JexlArithmetic.toLong(JexlArithmetic.java:906)
at org.apache.commons.jexl2.JexlArithmetic.compare(JexlArithmetic.java:718)
at org.apache.commons.jexl2.JexlArithmetic.greaterThanOrEqual(JexlArithmetic.java:824)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:785)
at org.apache.commons.jexl2.parser.ASTGENode.jjtAccept(ASTGENode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:186)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:95)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:338)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:483)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.buildVCfilters(VariantFiltration.java:474)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:379)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:318)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:99)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: For input string: "30.94"
##### ERROR ------------------------------------------------------------------------------------------