I encountered an issue when I use VariantsToTable. Thanks.

command:

Ref: hg19

    java -Djava.io.tmpdir=$tmp \
    -jar $GATK \
            -T VariantsToTable \
            -R $Ref \
            -V $InputDir/BQSR_AutosomeFilteredSNVs.vcf \
            -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F AC -F AN -F AF -F MQ \
            -GF FT -GF GT -GF AD -GF DP -GF GQ -GF PL -GF PGT -GF PID \
            -o $OutputDir/BQSR_AutosomeFilteredSNVs.table \
            2> $stderr/BQSR_filteredSNVs_toTable.stderr

ERROR --

ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.prettyPrintObject(VariantsToTable.java:370)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.addFieldValue(VariantsToTable.java:350)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.extractFields(VariantsToTable.java:334)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.map(VariantsToTable.java:213)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.map(VariantsToTable.java:108)
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:316)
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 3.7-0-gcfedb67):

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: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------