Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
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Entering edit mode
13 days ago
asalimih ▴ 60

Hello,
I'm annotating a deepvariant vcf file using vep ensembl version 110.1. however although the allele depth shows obvious heterozygous variant the ZYG output of vep when using --individual all shows HOM.
Here is the vcf (here I just put one variant) :

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422,assembly=38>
##contig=<ID=chr2,length=242193529,assembly=38>
##contig=<ID=chr3,length=198295559,assembly=38>
##contig=<ID=chr4,length=190214555,assembly=38>
##contig=<ID=chr5,length=181538259,assembly=38>
##contig=<ID=chr6,length=170805979,assembly=38>
##contig=<ID=chr7,length=159345973,assembly=38>
##contig=<ID=chr8,length=145138636,assembly=38>
##contig=<ID=chr9,length=138394717,assembly=38>
##contig=<ID=chr10,length=133797422,assembly=38>
##contig=<ID=chr11,length=135086622,assembly=38>
##contig=<ID=chr12,length=133275309,assembly=38>
##contig=<ID=chr13,length=114364328,assembly=38>
##contig=<ID=chr14,length=107043718,assembly=38>
##contig=<ID=chr15,length=101991189,assembly=38>
##contig=<ID=chr16,length=90338345,assembly=38>
##contig=<ID=chr17,length=83257441,assembly=38>
##contig=<ID=chr18,length=80373285,assembly=38>
##contig=<ID=chr19,length=58617616,assembly=38>
##contig=<ID=chr20,length=64444167,assembly=38>
##contig=<ID=chr21,length=46709983,assembly=38>
##contig=<ID=chr22,length=50818468,assembly=38>
##contig=<ID=chrX,length=156040895,assembly=38>
##contig=<ID=chrY,length=57227415,assembly=38>
##contig=<ID=chrM,length=16569,assembly=38>
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
chr3    195784506       .       A       AAG     18.6    PASS    .       GT:GQ:DP:AD:VAF:PL      1/1:12:45:14,27:0.6:18,13,0

The vep command I used:

 vep \
    --verbose --cache --offline --species homo_sapiens --assembly GRCh38 \
    --use_given_ref \
    --tab \
    --force_overwrite \
    --dir /opt/vep/.vep \
    --input_file /opt/vep/files/${inputVcf_file} \
    --output_file /opt/vep/files/${output_file} \
    --fasta /opt/vep/.vep/custom/references/Homo_sapiens_assembly38.fasta \
    --allele_number \
    --individual all \
    --per_gene

Why is this happening?
Thanks for any help in Advance

annotation vcf vep zygosity deepvariant • 154 views
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Entering edit mode

I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvariant side

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