Picard LiftoverVcf erroring

supfoolsupfool Member
edited July 2017 in Ask the GATK team

Hi,

java-jdk/1.8.0_92, picard/2.8.1

I'm trying to convert the coordinates of an exome vcf file (hg19) to a vcf with the latest reference's (grch38) coordinates. The command I use is below along with the error. The error is rather vague and I'm not sure what's going wrong. Can you help me? Thanks!

java -Xmx1G -jar ${PICARD} LiftoverVcf 
I=./17.2057_passedvariants_T99.9.vcf 
O=./17.2057_passedvariants_T99.9_chr38.p10.vcf 
CHAIN=./hg19ToHg38.over.chain 
REJECT=./17.2057_passedvariants_T99.9_chr38.p10.rejected.vcf 
R=./Homo_sapiens_assembly38_WithoutHaplotypes.fasta
[Mon Jul 17 14:07:46 CDT 2017] picard.vcf.LiftoverVcf INPUT=./17.2057_passedvariants_T99.9.vcf OUTPUT=./17.2057_passedvariants_T99.9_chr38.p10.vcf CHAIN=./hg19ToHg38.over.chain REJECT=./17.2057_passedvariants_T99.9_chr38.p10.rejected.vcf REFERENCE_SEQUENCE=./Homo_sapiens_assembly38_WithoutHaplotypes.fasta    WARN_ON_MISSING_CONTIG=false WRITE_ORIGI    NAL_POSITION=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
  2 [Mon Jul 17 14:07:46 CDT 2017] Executing as jdilts1@cri16cn083 on Linux 2.6.32-573.12.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14; Picard version: 2.8.1-SNAPSHOT
  3 INFO    2017-07-17 14:07:47     LiftoverVcf     Loading up the target reference genome.
  4 [Mon Jul 17 14:07:47 CDT 2017] picard.vcf.LiftoverVcf done. Elapsed time: 0.01 minutes.
  5 Runtime.totalMemory()=1029177344
  6 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  7 Exception in thread "main" java.lang.NullPointerException
  8         at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:158)
  9         at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
 10         at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
 11         at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

~

Post edited by shlee on

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @supfool,

    Picard LiftoverVcf recently got some updates. So please be sure to use v2.10.2. That being said, your error does not appear to be related to the recent fixes. It seems that you are missing either a file the tool expects, e.g. reference index or dictionary, or your input file contains variants that do not match up to the reference. Can you rerun your command with the latest Picard release and post the error? Thanks.

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