Option --no-escape doesn't work for custom annotation

[KevinMer]

Describe the issue

Hello,

I'm currently using custom annotation to retrieve upstream variant annotation. My custom annotation is a clinvar vcf that I processed to add p. informations from NCBI database.

I saw in options that --no-escape allows to deal with some annotations character (such as equal sign). However, I can see in my output vcf that equal sign is escaped for the custom annotation but not for the annotations retrieved from the cache.

I am using a singularity image with vep installed.

Do --no-escape option only work for cache annotation ? Is there a way to prevent escape for custom annotation ?

You can find in attachment a short example of my custom annotation and the corresponding input vcf.

Thanks for your help.

Kevin

Additional information

System

• VEP version: 110
• VEP Cache version: 110
• Perl version: 5.26.1
• OS: CentOS
• tabix installed ? : yes

Full VEP command line

vep 
--dir_cache /cache/dir 
--cache_version 110 
--format vcf 
--cache 
--refseq 
--offline 
--fasta /path/to/hg19_base.fa 
--hgvs 
--hgvsp_use_prediction 
--no_escape 
--custom file=custom.vcf.gz,short_name=ClinVar,format=vcf,type=exact,coords=0,fields=CLNHGVS%CLNHGVS_P 
-i input.vcf
-o output.vcf

Data files (if applicable)

They include:

• The input file : yes
• The output file : yes
• The custom file(s) : yes issueNoEscape.tar.gz

[likhitha-surapaneni]

Hi @KevinMer,

Currently,--no_escape is possible for HGVSp output field but not custom fields. Please let us know if this answers your question.

Kind regards, Likhitha

[KevinMer]

Hi @likhitha-surapaneni,

thanks for your answer.

Is there a trick I could use to keep the string integrity of the custom annotation ? I tried to replace all "=" by "\=" in order to avoid string escaping but it didn't work.

Would you have an idea to bypass this issue ?

Best regards, Kevin

[likhitha-surapaneni]

Hi @KevinMer ,

I am afraid it may not be possible to keep the string integrity for custom annotation fields. We have plans of extending --no_escape for HGVS strings in custom annotation fields in our coming releases.

Kind regards, Likhitha

[likhitha-surapaneni]

Hi @KevinMer , this is not in our immediate plans and hence I am closing this ticket for now. Please feel free to open a new issue if you have any further questions.