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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Error: unhandled exception: SyntaxError #116

Closed luceamso closed 2 years ago

luceamso commented 2 years ago

Hi Brent,

Thank you for sharing Slivar with the field. This is very useful.

While running Slivar on my VCF file to filter variants, I encountered the following issues and would like to ask you for help. The VCF file (cs_affected_fam.vcf.gz) was annotated with ANNOVAR databases including several customized ones, for instance, “gnomAD_r2.1.1_merged_all” and “bravo_freeze8” etc. (I have attached the list of databases used for ANNOVAR annotation). After several testings, I noticed that Slivar outputs the error when I tried to filter variants based on the “gnomAD_r2.1.1_merged_all” but it works fine with “bravo_freeze8“ which is another customized database (please see below). I would be grateful if you could look into this issue when you have a chance.

Thanks again. Seoon

gnomad brovo

INFO.txt

brentp commented 2 years ago

Hi, the problem is the attribute: gnomAD_r2.1.1_merged_all. You can't use the javascript . notation on that, but you can use, for example:

--info INFO['gnomAD_r2.1.1_merged_all'] < 0.001

this how you can access attributes with '.' or spaces in javascript.