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charite / jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)
http://jannovar.readthedocs.io/en/master/
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What does java.lang.NullPointerException means using VCF file #212

Closed frankMusacchia closed 8 years ago

frankMusacchia commented 8 years ago

Hi, I am using JAnnovar to annotate a VCF file after variant calling with GATK. The same file I used in Annovar without problems makes Jannovar complain like this:

_### ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console. Options verbosity: 1 dataFile: data/hg19_refseq.ser vcfFilePaths: [../ticlip_works/Trio_VN_CGH06/phasing_out/Trio_VN_CGH06_genot_varfilt_phasing.vcf] chromosomalChanges: [] showAll: true jannovarFormat: false writeJannovarInfoFields: false writeVCFAnnotationStandardInfoFields: true output infix: .jv INFO Deserializing JannovarData from data/hg19_refseq.ser INFO Deserialization took 6.64 sec. Annotating VCF... Exception in thread "main" java.lang.NullPointerException at de.charite.compbio.jannovar.annotation.Annotation.toVCFAnnoString(Annotation.java:268) at de.charite.compbio.jannovar.annotation.Annotation.toVCFAnnoString(Annotation.java:282) at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.applyStandardAnnotations(VariantContextAnnotator.java:250) at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.applyAnnotations(VariantContextAnnotator.java:238) at de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter.put(AnnotatedVCFWriter.java:103) at de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand.run(AnnotateVCFCommand.java:59) at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:111) _

What does this means?

Regards,

Francesco

holtgrewe commented 8 years ago

Hi Francesco, we are working on a solution to RefSeq making problems (actually we have a solution that is still pending validation).

In the meantime, please try to use Ensembl for annotating your variants.

I'll leave this issue open until we have the next release with a bug fix.

frankMusacchia commented 8 years ago

Ok. How can I use Ensembl or, even better, GenCode?

holtgrewe commented 8 years ago

Gencode is on our list but we don't have it yet.

Here is how to use Ensembl

# download ENSEMBL for hg19
java -jar jannovar-cli-0.16.jar download -d hg19/ensembl
# annotate using ENSEMBL
java -jar jannovar-cli-0.16.jar annotate -d data/hg19_ensembl.ser -i examples/small.vcf
visze commented 8 years ago

The problem should be fixed in the next release

holtgrewe commented 8 years ago

Version 0.17 is out, get it from Maven Central.

https://search.maven.org/#search%7Cga%7C1%7Cjannovar