Annotate VCF via VEP for gnomAD annotation considering FILTER column
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11 days ago
asalimih ▴ 60

Hello, I'm annotating a vcf file using ensembl vep and gnomad v4 vcf file:

 vep --cache --offline --species homo_sapiens --assembly GRCh38 \
     --input_file input.vcf \
     --custom gnomad.vcf.bgz,gnomADg,vcf,exact,0,AF

because the gnomad.vcf.bgz file contains all variants including low quality ones (specified in the FILTER column with different labels), the output will annotate disregarding the FILTER column of the gnomad vcf file. I know one way is to only keep PASS variants on gnomad vcf file but I want to annotate with all of them plus the gnomad FILTER label in the output.
One way is to make another custom file containing the gnomad FILTER info as a feature. Is there any better way for this? Thanks in Advance

vep vcf gnomad • 123 views
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