If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.