Hi,
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
Best,
ernesto