This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to filter VEP results of "missing values"

Hello,

I have a VEP annotated VCF files with CADD and LOFTEE annotations. I need to filter in results with either CADD score >= 20 OR LOFTEE HC without any flag

My code is as following

filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf --force_overwrite --filter "CADD_PHRED >= 20 or (LoF = HC and LoF_filter = . and LoF_flags = .)"

I guess the problem is that "LoF_filter" and "LoF_flags" should be blank (no value) but I am not sure how I should express this in the code (I tried = "" but still not working)?

Thank you very much

filter vep
• 1,902 views • link
updated by GenoMax GenoMax • written by YL • YL

Have you tried with a space between the " "?

• 0 views • link
written by GenoMax GenoMax

The VEP dose not seem to recognize " ". It returned "MSG: ERROR: Error parsing filter string - incomplete parentheses sets?"

• 0 views • link
written by YL • YL

1 answer

Thank you so much!

I found an error with my code. And this works:

filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf --force_overwrite --filter "(CADD_PHRED >= 20 and LoF = "") or (LoF = HC and LoF_filter = "" and LoF_flags = "")"
• 0 views • link
updated by GenoMax GenoMax • written by YL • YL

Log in to answer this question.

More posts like this