Liftover error from picard

Question

[GK1610]

I am trying to align sample genotypes from hg19 to hg38. To do so, I am using liftover from picard on my_vcf_genotype_file (VCF file)

chainfile=hg19ToHg38.over.chain.gz
java -jar  picard-tools-2.5.0/picard.jar LiftoverVcf I=$my_vcf_genotype_file O=$my_vcf_genotype_file.hg38.vcf.gz C=$chain_file REJECT=trash.vcf.gz R=GRCh38.primary_assembly.genome.fa

I am getting this error

INFO    2018-07-05 18:54:28 LiftoverVcf Loading up the target reference genome.
INFO    2018-07-05 18:54:48 LiftoverVcf Lifting variants over and sorting.
ERROR   2018-07-05 18:54:56 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target reference.

Can you help me to resolve this?

Answer 1

[h.mon]

Try adding WARN_ON_MISSING_CONTIG=true ( Picard liftoverVCF error when attempting to liftover to build 38 ), but you also should check if the chain files are from the exact same version as the genome you are using - the error is complaining there are contigs differences between genomes and chain files.

[GK1610]

I am getting this error now

INFO 2018-07-06 11:52:13 LiftoverVcf Loading up the target reference genome. INFO 2018-07-06 11:52:59 LiftoverVcf Lifting variants over and sorting. WARNING 2018-07-06 11:53:06 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr14_GL000009v2_random that is not part of the target reference. [Fri Jul 06 11:59:17 EDT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 7.08 minutes. Runtime.totalMemory()=9411493888

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at htsjdk.variant.variantcontext.GenotypeBuilder.make(GenotypeBuilder.java:192) at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:736) at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128) at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:347) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:161) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:194) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:136) at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:206) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)