Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

VariantsToBinaryPed Throwing IndexOutofBoundsException

tottlefieldstottlefields Newmarket, UKMember
edited April 2017 in Ask the GATK team

Hi All,

I am trying to use the GATK v3.7 VariantsToBinaryPed on my multi-sample VCF file to create PLINK files. However it is throwing an error, the stack trace is shown below...

##### ERROR --
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -1
        at htsjdk.variant.variantcontext.GenotypeLikelihoods.getGQLog10FromLikelihoods(GenotypeLikelihoods.java:220)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.checkGQIsGood(VariantsToBinaryPed.java:442)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getStandardEncoding(VariantsToBinaryPed.java:406)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getEncoding(VariantsToBinaryPed.java:398)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.writeIndividualMajor(VariantsToBinaryPed.java:282)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:267)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:103)
        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: -1
##### ERROR ------------------------------------------------------------------------------------------

My command...

java -Xmx32g -Djava.io.tmpdir=$HOME/javatempdir -jar /opt/gatk3.7/GenomeAnalysisTK.jar \
        -T VariantsToBinaryPed \
        -R /geneticsdata/alces-flight-image/canfam3/ensembl/canfam3.fasta \
        -V /geneticsdata/wgs_ens/ens_WGS_87_VEP.vcf.gz \
        --minGenotypeQuality 10 \
        -m /geneticsdata/wgs_ens/ens_WGS_87_metadata.fam \
        -bed /geneticsdata/wgs_ens/ens_WGS_87.bed \
        -bim /geneticsdata/wgs_ens/ens_WGS_87.bim \
        -fam /geneticsdata/wgs_ens/ens_WGS_87.fam

The line of the VCF file where the script is falling over...

1       668     .       C       T       153.78  .       AC=7;AF=0.233;AN=30;BaseQRankSum=-7.270e-01;ClippingRankSum=0.727;DP=48;ExcessHet=0.0117;FS=0.000;InbreedingCoeff=0.3446;MLEAC=7;MLEAF=0.233;MQ=33.46;MQ0=0;MQRankSum=0.727;QD=25.63;ReadPosRankSum=0.727;SOR=0.368;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||||||SNV||||||||||||||||||||||||||||||||||      GT:AD:DP:GQ:PGT:PID:PL  0/0:1,0:1:3:.:.:0,3,31  0/0:1,0:1:3:.:.:0,3,32  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,57  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,65  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:16,0:16:45:.:.:0,45,675     ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   1/1:0,3:3:9:.:.:92,9,0  1/1:0,1:1:3:.:.:10,3,0  1/1:0,3:3:9:.:.:102,9,0 0/1:3,1:4:8:0|1:668_C_T:8,0,58  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,21  ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,12  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:8,0:8:18:.:.:0,18,270       ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,30  0/0:1,0:1:3:.:.:0,3,34  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:1,0:1:.:.:.:0,0,0      0/0:1,0:1:3:.:.:0,3,32  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0

I'm probably doing something totally stupid (apologies if I am), but please can somebody help me out?

Thanks,
Ellen.

Answers

Sign In or Register to comment.