Dear GATK team,
I'm working on the VQSR step, and the inbreedingcoeff given as recommend annotation. Since it can only be annotated when there are >10 samples, so I merged my 35 samples' MuTect2 output vcf files, then apply VariantAnnotator to the merge vcf for inbreedingcoeff annotation. The command finished normally, but there are no inbreedingcoeff annotation in output. Why could this happen?
My command for VariantAnnotator:
java -jar /home/yangxx/software/GATK-3.5/GenomeAnalysisTK.jar -T VariantAnnotator -R /home/yangxx/hg38bundle/Homo_sapiens_assembly38.fa -V /home/yangxx/PIH/GATK-rerun/PHPRcom-VarAno.vcf -L /home/yangxx/PIH/GATK-rerun/PHPRcom-VarAno.vcf -o /home/yangxx/PIH/GATK-rerun/PHPRcom-VarAno-2.vcf -D /home/yangxx/hg38bundle/Homo_sapiens_assembly38.dbsnp138.vcf -A InbreedingCoeff -U ALLOW_N_CIGAR_READS
Thanks for any help!