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Picard LiftoverVcf: contig not part of the target reference

ryhuiryhui CambridgeMember

Dear GATK team,

I am trying to liftover a vcf file from hg19 to hg38, by running the command
java -jar ~/tools/picard-2.1.0/dist/picard.jar LiftoverVcf I=input.chr22.vcf O=hg38.chr22.vcf CHAIN=hg19ToHg38.over.chain REJECT=liftover_rejected.chr22.vcf R=chr22.fa

Since I'm working on one chromosome only, my vcf file has only "chr22" in the CHROM field. chr22.fa, the reference genome in hg38, starts with ">chr22" on the first line. I also generated the .dict file for it using Picard tools. chr22.dict file looks like:
@HD VN:1.5 SO:unsorted
@SQ SN:chr22 LN:50818468 M5:221733a2a15e2de66d33e73d126c5109 UR:file:/my/directory/chr22.fa

However, after a few seconds I always get the following error message:
[Thu Feb 18 15:53:08 GMT 2016] Executing as [email protected] on Linux 3.2.0-75-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_73-b02; Picard version: 2.1.0() JdkDeflater
INFO 2016-02-18 15:53:09 LiftoverVcf Loading up the target reference genome.
INFO 2016-02-18 15:53:11 LiftoverVcf Lifting variants over and sorting.
ERROR 2016-02-18 15:53:11 LiftoverVcf Encountered a contig, chr22 that is not part of the target reference.

Could you suggest how to fix this? Thank you!

Best,
Ruoyun

Issue · Github
by Sheila

Issue Number
609
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
dekling

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