Keep Format and Individual fields after annotating VCF with VEP
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3.2 years ago
MasMarius ▴ 10

Hi, I got stuck, my intention was to use VEP on my VCF and later do a VariantsToTable, but annotations of VEP are added to a field into INFO called CSQ and I can not figure out how to get them as VariantsToTable does with INFO column. Any idea how to extract it using VariantsToTable from GATK or better suggestion?

Thanks in advance!

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VEP VCF annotation INFO CSQ • 1.4k views
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What are you trying to do with the data overall? Why is the data being in the CSQ field a problem?

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Hi Emily, It is not a problem, just want to switch it into a more readable for EXCEL/CALC. Converting CSQ (info) to a column with each vep annotation following a order such as CHROM,QUAL,Feature,Biotype,GNOMAD,Consequence.. and i will like to know if, does exists any tool for it?

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