Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
gcy0115 opened this issue Feb 15, 2023 · 0 comments
Open

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

gcy0115 opened this issue Feb 15, 2023 · 0 comments

Comments

@gcy0115
Copy link

gcy0115 commented Feb 15, 2023

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@gcy0115