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VariantAnnotator is not annotating variants with InbreedingCoeff

ernestoernesto HinxtonMember


I am using GATK VariantAnnotator to annotate my VCF with the InbreedingCoeff but when I check the output VCF I see that no variant was annotated with the InbreedingCoeff.

I've used a pedigree file in the .ped format and my VCF has more than 10 samples.

You can see here the command line I've used:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R ${ref.fa} -V ${input.vcf.gz} --annotation Coverage --annotation QualByDepth --annotation FisherStrand --annotation StrandOddsRatio --annotation RMSMappingQuality --annotation MappingQualityRankSumTest --annotation ReadPosRankSumTest --annotation InbreedingCoeff --annotation ChromosomeCounts -I bamfiles.list -L ${input.vcf.gz} -ped ${file.ped} |bgzip -c > ${out.vcf.gz}

And the first lines of the ${file.ped}:
$ head -n 10 ${file.ped}
HG00096 HG00096 0 0 1 0
HG00097 HG00097 0 0 2 0
HG00098 HG00098 0 0 1 0
HG00099 HG00099 0 0 2 0
HG00100 HG00100 0 0 2 0
HG00101 HG00101 0 0 1 0
HG00102 HG00102 0 0 2 0
HG00103 HG00103 0 0 1 0
HG00104 HG00104 0 0 2 0
HG00105 HG00105 0 0 1 0

Also, I've attached the VCF I have used as ${input.vcf.gz}

GATK version: version 3.7-0-gcfedb67




  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi ernesto,
    Can you confirm this happens even if you only request the InbreedingCoeff annotation by itself (without all other annotations)? Also, GATK4 latest release has VariantAnnotator in it. If you could test that as well, that would be great.

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