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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 http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:133)
at htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:83)
at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:93)
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:188)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

Any idea how to solve it?

Best Answer


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