Keep Format and Individual fields after annotating VCF with VEP

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5.6 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!

VEP VCF annotation INFO CSQ • 2.0k views

ADD COMMENT • link 5.6 years ago by MasMarius ▴ 10

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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?

ADD REPLY • link 5.6 years ago by Emily 23k

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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?

ADD REPLY • link 5.6 years ago by MasMarius ▴ 10

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