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Why GATK 3.7 VariantAnnotator - Processed 0 loci

I was trying to use GATK 3.7 VariantAnnotator to annotate a vcf.gz file. Here is my code:

/u/local/apps/java/jdk1.8.0_111/bin/java -jar /u/local/apps/gatk/3.7/GenomeAnalysisTK.jar \
-T VariantsToBinaryPed \
-R $FASTA \
-V ${NAME}_dbsnp-GRCh37.vcf \
-m ${HOME}/raw/0.2_SCZ.fam \
-bed ${NAME}.bed \
-bim ${NAME}.bim \
-fam ${NAME}.fam \
-mgq 0 \
-mode SNP_MAJOR

But the output file was extremely small, and then in the error log I found the following:

Note that "INFO 15:07:00,074 VariantAnnotator - Processed 0 loci." at the end of all the records of ProgressMeter.

How shall I fix this?
Thanks,
Jenny

Answers

  • Sorry, I was using the following script:

    /u/local/apps/java/jdk1.8.0_111/bin/java -jar /u/local/apps/gatk/3.7/GenomeAnalysisTK.jar \
    -R $FASTA \
    -T VariantAnnotator \
    -V $VCF \
    -o ${NAME}_dbsnp-GRCh37.vcf \
    --alwaysAppendDbsnpId \
    --dbsnp $DBSNP \
    --unsafe LENIENT_VCF_PROCESSING

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Jennybear
    Hi Jenny,

    Can you check the output VCF and make sure the dbsnp rsid field is populated?

    Thanks,
    Sheila

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