How to annotate only closest SNP using SnpEff?

Hello everyone! I am trying to annotate only the closest SNP using SnpEff software with the following command:

java -Xmx16G -jar snpEff.jar closest organismDB my.vcf > my.annot.closest.vcf

However when I then try to extract the fields into a table using such command:

cat my.annot.closest.vcf | ./scripts/vcfEffOnePerLine.pl | java -jar  SnpSift.jar extractFields - CHROM POS ID AF "CLOSEST[*]GENEID" > my.annot.closest.vcf.txt

I am getting a lot of columns instead of the five: CHROM, POS, ID, AF, GENEID. If anyone faced such problem please help!

snpeff annotation snp

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written 6.7 years ago by rimgubaev

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