extract "ANN[*].RANK" from the ANN field

Open gcy0115 opened this issue 2 years ago • 0 comments

Hi,

I have a vcf file annotated by snpeff and want to extract "ANN[*].RANK" from the ANN field like

ANN=G|missense_variant|MODERATE|TNN|ENSG00000120332|transcript|ENST00000239462|protein_coding|13/19|c.3038C>G|p.Thr1013Arg|3151/5008|3038/3900|1013/1299||

java -jar /home/pmi/src/snpEff/SnpSift.jar extractFields my.vcf CHROM POS ID REF ALT "ANN[*].RANK"

but I got 13 not 13/19 for ANN[*].RANK.

Thanks

Feb 15 '23 07:02 gcy0115