Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

HaplotypeCaller problems with ploidy argument

I am trying to use the HaplotypeCaller with a ploidy setting of 1 to genotype sex chromosomes in a single individual using the following command:

java -Xmx4g -jar ~/applications/GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller -R /data/genome_references/Hmel1-1_primaryScaffolds_mtDNA.fasta -L Z_chromosome.intervals -ploidy 1 -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -I realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.bam -hets 0.01 -indelHeterozygosity 0.01 -out_mode EMIT_ALL_CONFIDENT_SITES -maxAltAlleles 1 -o realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.HC_sex.vcf

This is failing. Error message at the bottom.

Setting ploidy to 2 works fine.

The following command with the UnifiedGeonotyper is also fine:

java -Xmx4g -jar ~/applications/GenomeAnalysisTK-3.2-2.jar -T UnifiedGenotyper -R /data/genome_references/Hmel1-1_primaryScaffolds_mtDNA.fasta -ploidy 1 -L Z_chromosome.intervals -I realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.bam -glm BOTH -hets 0.01 -indelHeterozygosity 0.01 -out_mode EMIT_ALL_CONFIDENT_SITES -o realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.HC_sex.vcf

Any ideas what the problem is?

Thanks,
Kanchon

INFO 12:42:20,180 AFCalcFactory - Requested ploidy 1 maxAltAlleles 6 not supported by requested model EXACT_INDEPENDENT looking for an option
INFO 12:42:20,181 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY
INFO 12:42:21,550 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.assignGenotype(GeneralPloidyExactAFCalc.java:559)
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.subsetAlleles(GeneralPloidyExactAFCalc.java:527)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:286)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:335)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:320)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:310)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.isActive(HaplotypeCaller.java:844)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.addIsActiveResult(TraverseActiveRegions.java:618)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.access$800(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:378)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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

Best Answer

Answers

Sign In or Register to comment.