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All de-novo mutations are 0/1 from genotype refinement workflow

siriansirian USMember ✭✭
edited May 1 in Ask the GATK team

Hi,

I have a vcf from a trio and ran genotype refinement workflow by following the steps described at: https://software.broadinstitute.org/gatk/documentation/article.php?id=4727

My purpose was to identify the new mutations in the child compared to the parents. The final step I ran was:

gatk --java-options "-Xmx100g" VariantAnnotator -R ${genome_fasta} -V input_trioGP_GQfiltered.vcf -A PossibleDeNovo -ped trio.ped -o input_trioGP_GQfiltered_deNovos.vcf

All the mutations annotated as "hiConfDeNovo" or "loConfDeNovo" have the same genotypes in the trio: 0/1 in child and 0/0 in parents. Is this normal? I was expecting some sites like 0/2 (in child) 0/1 (in parents) would also be picked. Are multi-allele sites simply omitted by this tool?

Thanks,

Post edited by sirian on

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