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Nightly build: SelectVariants doesn't appear to work on Haploid VCFs

I'm running the nightly build on ubuntu 16.04, and I have a problem using SelectVariants on Haploid vcf's

I found this closed issue on a similar problem, but I have no * alleles in my vcf file, so it might be unrelated http://gatkforums.broadinstitute.org/gatk/discussion/7231/selectvariants-doesnt-appear-to-work-on-haploid-vcfs

Please let me know if there is a specialized forum or process to report problems with the nightly build. I apologize for not formatting this post properly, for some reason the formatting tools do not show up.

$ java -version
openjdk version "1.8.0_91"
OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-0ubuntu4~16.04.1-b14)
OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)

$ gatk --version

java -jar GenomeAnalysisTK.jar \
-T SelectVariants \
-R /usr/share/ngs/Reference/NC_011083.fasta \
-V j105.vcf \
-o j105_629b2714.2vcf \
--excludeNonVariants \
--removeUnusedAlternates \
-select "AF<1.0" \
-sn 102757-001-022 \
-sn 102757-001-024 \
-sn 102757-001-026

INFO 08:41:49,435 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 08:41:49,436 HelpFormatter - The Genome Analysis Toolkit (GATK) vnightly-2016-06-01-gf72aaad, Compiled 2016/06/01 00:01:16
INFO 08:41:49,436 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 08:41:49,436 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 08:41:49,437 HelpFormatter - [Wed Jun 01 08:41:49 CEST 2016] Executing on Linux 4.4.0-22-generic amd64
INFO 08:41:49,437 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-0ubuntu4~16.04.1-b14 JdkDeflater
INFO 08:41:49,439 HelpFormatter - Program Args: -T SelectVariants -R /usr/share/ngs/Reference/NC_011083.fasta -V j105.vcf -o j105_629b2714.2vcf --excludeNonVariants --removeUnusedAlternates -select "AF<1.0" -sn 102757-001-022 -sn 102757-001-024 -sn 102757-001-026
INFO 08:41:49,442 HelpFormatter - Executing as [email protected] on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_91-8u91-b14-0ubuntu4~16.04.1-b14.
INFO 08:41:49,443 HelpFormatter - Date/Time: 2016/06/01 08:41:49
INFO 08:41:49,443 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 08:41:49,443 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 08:41:49,453 GenomeAnalysisEngine - Strictness is SILENT
INFO 08:41:49,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 08:41:49,562 GenomeAnalysisEngine - Preparing for traversal
INFO 08:41:49,563 GenomeAnalysisEngine - Done preparing for traversal
INFO 08:41:49,564 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 08:41:49,564 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 08:41:49,567 SelectVariants - Including sample '102757-001-022'
INFO 08:41:49,567 SelectVariants - Including sample '102757-001-024'
INFO 08:41:49,567 SelectVariants - Including sample '102757-001-026'

ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: All samples must be diploid
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.getDiploidLikelihoodIndexes(GATKVariantContextUtils.java:688)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.determineDiploidLikelihoodIndexesToUse(GATKVariantContextUtils.java:647)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.fixDiploidGenotypesFromSubsettedAlleles(GATKVariantContextUtils.java:1421)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.updatePLsSACsAD(GATKVariantContextUtils.java:1403)
at org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants.subsetRecord(SelectVariants.java:1080)
at org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants.map(SelectVariants.java:854)
at org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants.map(SelectVariants.java:309)
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:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2016-06-01-gf72aaad):
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://www.broadinstitute.org/gatk
ERROR MESSAGE: All samples must be diploid

Best Answer


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