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pcingola / SnpSift

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extract "ANN[*].RANK" from the ANN field #82

Open gcy0115 opened 1 year ago

gcy0115 commented 1 year ago

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