Question: Keep Format and Individual fields after annotating VCF with VEP
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gravatar for MasMarius
17 months ago by
MasMarius10
MasMarius10 wrote:

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!

CLOSE RELATED TO:Keep Format and Individual fields when annotating VCF with VEP

info csq vep annotation vcf • 690 views
ADD COMMENTlink written 17 months ago by MasMarius10
1

What are you trying to do with the data overall? Why is the data being in the CSQ field a problem?

ADD REPLYlink written 17 months ago by Emily_Ensembl20k

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 REPLYlink written 17 months ago by MasMarius10
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