VCF and pedigree info

Hi,

I have a trio WES data that I'm trying to run mendelian error rate with RTG tools.

Following the GATK best practices, I ran BWA, SortSam, Marduplicates, BaseRecalibrator, BQSR, and HaplotypeCaller, though at haplotypecaller I want gvcf so I ran the trio data separately.

gatk HaplotypeCaller -R ./Homo_sapiens_assembly38.fasta -I WBTB-001A.sort.dup.gatk.recal.bqsr.bam -ERC GVCF -L ./truseq-exome-targeted-regions-manifest-v1-2.hg38.bed --dbsnp ./Homo_sapiens_assembly38.dbsnp138.vcf -O WBTB-001A.g.vcf.gz


Then I ran CombineGVCFs and GenotypeGVCFs

gatk CombineGVCFs -R ./Homo_sapiens_assembly38.fasta --variant ./gatk2.001A/WBTB-001A.g2.vcf --variant ./gatk2.001B/WBTB-001B.g2.vcf --variant ./gatk2.001C/WBTB-001C.g2.vcf -o ./gatk/gatk2.WBTB-001.c.g.vcf

gatk GenotypeGVCFs -R ./Homo_sapiens_assembly38.fasta --variant ./gatk/gatk2.cgvcf/gatk2.WBTB-001.c.g.vcf -O ./gatk/gatk2.WBTB-001.gatk.genotype.vcf

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For RTG mendelian I created a pedigree file (tab-delimited) WBTB-001.ped,

WBTB-001 A B C 1 2
WBTB-001 B 0 0 1 1
WBTB-001 C 0 0 2 1

./tools/rtg-tools/dist/rtg-tools-3.9.1-6dde278/rtg mendelian -i ./gatk/gatk2.WBTB-001.gatk.genotype.vcf -t ./ref/ref.hg38.sdf/ --pedigree=./WBTB-001.ped > ./gatk/WBTB.001.gatk.results.txt

However, it came back with "No family information found, no checking done."


Just wondering if I had missed a step for incorporating pedigree info into the VCFs.
Could you give us some suggestions on how to solve this?

Thank you