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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Filter by gene using the command line version #300

Closed BologaAlexandru closed 4 days ago

BologaAlexandru commented 1 week ago

Hello,

I was wondering if the Gene Filter can be used in command line. I am running oc on a WGS vcf file and my command looks like this:

oc run file.vcf -l hg19 -a clinvar -t text excel

The text/excel output contains all genomic variants from the input vcf. Is there a way to generate a similar output but using the Gene Filter too, without open the oc gui?

I tried to use the filtersqlite option after I saved the filter (a list of genes) from the gui as .json file with the command:

oc util filtersqlite file.vcf.sqlite -f filter_by_gene.json -s filtered

Unfortunetly, I couldn't obtain a new text/excel file for my vcf with the Gene Filter applied without using the oc gui. Is this possible?

Thank you!

jasminebro commented 1 week ago

Hi @BologaAlexandru. The oc report function is the easiest way to filter without using the GUI. I have shared the documentation for generating a report here (Generate a Report from a Job)

Can you try this command and let me know if it works? oc report input.sqlite -f genefilter.json -t excel

Thank you for using OpenCRAVAT!

BologaAlexandru commented 1 week ago

Hello @jasminebro Thank you for your answers. The oc report function is working.

Thank you again! Wish you all the best!

jasminebro commented 4 days ago

@BologaAlexandru Awesome! Happy to hear it. Please let us know if you need any further assistance and thank you for using OpenCRAVAT!

If you have 2 minutes, please click on the following link to access our user feedback form: https://tinyurl.com/OpenCRAVATUserSurvey . We are always eager to receive feedback from our users. Happy annotating!