Hi all,
Has anyone else gotten the following:
java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:306) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:35) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
My command line was: java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -f "mom+dad=child" -R hg19.fa
Cheers,
Paul
