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)