LiftoverVcf no output
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Entering edit mode
2.1 years ago
brismiller ▴ 40

Hey all,

I am trying to run Picard's LiftoverVcf to lift over a hg19 to hg38, but there is no output. It runs with no errors, but it doesn't make the output files. Any help would be appreciated.

Here is the relevant section of the script used. I even tried unzipping all input files, but no output files are produced.

# $1 is the input vcf to the script    
java -jar /home/groups/prime-seq/pipeline_tools/bin/picard.jar LiftoverVcf \
    I=$1 \
    O=$output_vcf \
    CHAIN=/home/path/common_files/hg19ToHg38.over.chain \
    REJECT=$output_reject_vcf \
    R=/home/path/genomes/GCF_000001405.39_GRCh38.p13_genomic.fna

Here is the output.

    INFO    2020-06-01 17:22:33 LiftoverVcf Loading up the target reference genome.
[Mon Jun 01 17:22:33 PDT 2020] picard.vcf.LiftoverVcf done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2039414784
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
    at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:287)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Assembly genome liftover sequencing picard • 964 views
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Entering edit mode

you cannot have such error at line 287 for picard LiftoverVcf: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/vcf/LiftoverVcf.java#L287 . Please, retry with the latest version of picard.

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