Hi,
I am trying to covert a vcf file to a bed file using VariantsToBinaryPed. Input: vcf file and metadata file. Error below. Can anyone advise? Thanks!
[umcv@node021 unag]$ java -jar /data4/una/GenomeAnalysisTK.jar -T VariantsToBinaryPed -R /data4/una/unag/index/human_g1k_v37.fasta -V GTEx.vcf -m GTEx.fam -bed output.bed -bim output.bim -fam output.fam -mgq 0
INFO 10:54:37,479 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,482 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 10:54:37,482 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 10:54:37,483 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 10:54:37,483 HelpFormatter - [Tue May 23 10:54:37 BST 2017] Executing on Linux 2.6.18-404.el5 amd64
INFO 10:54:37,483 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13
INFO 10:54:37,490 HelpFormatter - Program Args: -T VariantsToBinaryPed -R /data4/una/unag/index/human_g1k_v37.fasta -V GTEx.vcf -m GTEx.fam -bed output.bed -bim output.bim -fam output.fam -mgq 0
INFO 10:54:37,496 HelpFormatter - Executing as umcv@node021 on Linux 2.6.18-404.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13.
INFO 10:54:37,497 HelpFormatter - Date/Time: 2017/05/23 10:54:37
INFO 10:54:37,498 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,498 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,517 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:54:37,793 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 12:55:58,987 RMDTrackBuilder - Writing Tribble index to disk for file /data4/una/unag/GTEx.vcf.idx
INFO 12:56:03,976 GenomeAnalysisEngine - Preparing for traversal
INFO 12:56:03,987 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:56:03,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:56:03,989 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:56:03,989 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
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)