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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.
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.
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.
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
Full VEP command line
Data files (if applicable)
They include:
issueNoEscape.tar.gz
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