Funcotator returns a nullpointer exception when trying to output compressed VCF
open | Created 2019-02-15 | Last updated 2019-07-01| Posted by fpbarthel | See in Github

Engine Funcotator bug

Bug Report

Affected tool(s) or class(es)


Affected version(s)

GATK release


Funcotator returns a NullPointerException when trying to output compressed VCF:

15:35:26.085 INFO  Funcotator - Creating a VCF file for output: XXXX
15:35:26.125 INFO  ProgressMeter - Starting traversal
15:35:26.125 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
log4j:WARN No appenders could be found for logger (
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See for more info.
15:35:26.328 INFO  Funcotator - Shutting down engine
[February 15, 2019 3:35:26 PM EST] done. Elapsed time: 0.18 minutes.
        at htsjdk.tribble.index.tabix.TabixIndexCreator.finalizeFeature(
        at htsjdk.tribble.index.tabix.TabixIndexCreator.finalizeIndex(
        at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(
        at htsjdk.variant.variantcontext.writer.VCFWriter.close(
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(
        at org.broadinstitute.hellbender.Main.mainEntry(
        at org.broadinstitute.hellbender.Main.main(

Steps to reproduce

Does not work

gatk Funcotator --variant input.vcf.gz --reference /path/to/human_g1k_v37_decoy.fasta --ref-version hg19 --data-sources-path /path/to/funcotator_dataSources.v1.6.20190124s/ --output output.vcf.gz --output-file-format VCF


gatk Funcotator --variant input.vcf.gz --reference /path/to/human_g1k_v37_decoy.fasta --ref-version hg19 --data-sources-path /path/to/funcotator_dataSources.v1.6.20190124s/ --output output.vcf --output-file-format VCF

(note that the --output parameter is different)

Expected behavior

It should either give an error/warning saying outputting compressed VCF output is not supported, or output a compressed VCF like other GATK tools

Actual behavior

See examples above

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