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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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missing null frequency variants #136

Closed luceamso closed 2 years ago

luceamso commented 2 years ago

hi, Brent

I use "gnomAD_r2.1.1_merged_all" as one of the info attributes. It's working well because you told me how to apply this before. But I realized that null frequency is not recognized. Filtering by numbers works just fine. I've tried several things, but nothing worked. Below are what I've tried:

--info "INFO['gnomAD_r2.1.1_merged_all'] == '.'"
instead of '." : '[.]', ['.'], "\\.", "\."
--info 'INFO["gnomAD_r2.1.1_merged_all"] == "."'
instead of '." : "[.]", ["."], "\\.", "\."

I would like to ask for help on this.

brentp commented 2 years ago

What does the VCF header look like for this field?

luceamso commented 2 years ago

oh, it's float. I was confused by looking at the other field.

I solved the problems. thank you!