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!