The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

GATK: java.lang.NullPointerException

gatkuser8832gatkuser8832 Member
edited September 2018 in Ask the GATK team

my command:
java -jar ~/Desktop/gatk- 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.
To get help, see
    at picard.vcf.LiftoverVcf.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(
    at org.broadinstitute.hellbender.Main.mainEntry(
    at org.broadinstitute.hellbender.Main.main(

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

Best Answer


Sign In or Register to comment.