GATK4beta6 HaplotypeCaller doesn't index g.vcf.gz output

With the following command:

java -Xmx7g -jar gatk-package-4.beta.6-local.jar HaplotypeCaller -ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation --maxReadsPerAlignmentStart 0 -GQB 5 -GQB 10 -GQB 15 -GQB 20 -GQB 25 -GQB 30 -GQB 35 -GQB 40 -GQB 45 -GQB 50 -GQB 55 -GQB 60 -GQB 65 -GQB 70 -GQB 75 -GQB 80 -GQB 85 -GQB 90 -GQB 95 -GQB 99 -I example.bam -O example.g.vcf.gz -R /path/to/GRCh38.d1.vd1.fa

the output file example.g.vcf.gz does not get indexed, despite the default value for --createOutputVariantIndex being True. The command finishes successfully without error, but never creates the index. '

Ben

Best Answer

  • shleeshlee CambridgeMember, Broadie, Moderator
    Accepted Answer

    Hi @bkelly01,

    I can recapitulate your observation. HaplotypeCaller in GATK4.beta hasn't been tied out yet and I assume this is an issue that will be fixed in the official release. You can use IndexFeatureFile to index the .g.vcf.gz in the meanwhile. If you still do not get an index with the official release, please let us know.

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator
    Accepted Answer

    Hi @bkelly01,

    I can recapitulate your observation. HaplotypeCaller in GATK4.beta hasn't been tied out yet and I assume this is an issue that will be fixed in the official release. You can use IndexFeatureFile to index the .g.vcf.gz in the meanwhile. If you still do not get an index with the official release, please let us know.

  • bkelly01bkelly01 USAMember

    It was more of a "call to your attention" than anything else. I went the tabix -p vcf my.g.vcf.gz route because I didn't realize IndexFeatureFile existed. Thanks!

  • shleeshlee CambridgeMember, Broadie, Moderator

    Thanks @bkelly01 for taking the time to call our attention to this. The fix for HaplotypeCaller indexing was incorporated in November and should be available for the next release.

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