To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Problem with LiftoverVcf

ViscardiViscardi Porto AlegreMember

It is my first time running the LiftoverVcf, but I saw that many other users passed through difficulties similar to mine but not exactly the same. I'm trying to convert a vcf file from Hg18 to Hh19.

java -jar picard.jar LiftoverVcf I=input.vcf O=out.chr21.vcf CHAIN=hg18ToHg19.over.chain REJECT=rejected_variants.chr21.vfc R=hg19.fasta

It seems that the inputs are ok and that there is also no problem with the vcf nor with the reference.

This is the ERROR message:

INFO 2017-10-26 23:33:39 LiftoverVcf Loading up the target reference genome.
[Thu Oct 26 23:33:50 BRST 2017] picard.vcf.LiftoverVcf done. Elapsed time: 0.19 minutes.
To get help, see
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.reference.FastaSequenceFile.readSequence(
at htsjdk.samtools.reference.FastaSequenceFile.nextSequence(
at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(
at picard.vcf.LiftoverVcf.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(

Any idea how to solve it?

Best Answer


Sign In or Register to comment.