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GATK: java.lang.NullPointerException

gatkuser8832gatkuser8832 Member
edited September 2018 in Ask the GATK team

my command:
java -jar ~/Desktop/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar LiftoverVcf -I input.vcf -O input_lifted.vcf -C ~/Desktop/hg38ToHg19.over.chain --REJECT rejected.vcf -R ~/Desktop/Homo_sapiens.GRCh37.dna.primary_assembly.fa

It seems to execute fine at first, but then it ends with:

[Thu Sep 20 15:01:12 CEST 2018] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=819986432
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.NullPointerException
    at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:287)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

(and by the way, the documentation says you can use something like "I=input.vcf" which is not true -> "Invalid argument 'I=input.vcf'")

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