Improvements to documentation and scripts

genome-nexus / annotation-tools

Tools developed for AACR GENIE to allow annotation of vcf and maf files from a number of centers and merging the results

MIT License

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Improvements to documentation and scripts #46

Closed ruslan-forostianov closed 1 year ago

ruslan-forostianov commented 2 years ago

Write a data error report file
Match FUNC INFO field exactly
Add python dependencies file and document how to use it
Add example on how to run annotation_suite_wrapper script
Document how to create a trust store and import certificates

ruslan-forostianov commented 2 years ago

@ao508 @inodb @sheridancbio Hey guys, sorry for the late replies. I had my answers pending as I forgot to submit them.

ruslan-forostianov commented 1 year ago

Thank you, @sheridancbio ! Please let me know if the "FUNC" parsing change won't work for you. We'll find the way.

ruslan-forostianov commented 1 year ago

Thanks for the documentation updates. Let's wait until January 27, 2023 before squash/merging this PR into the master branch to give a chance for our SAGE collaborator to take a look at the issue related to "FUNC" in an INFO field key. My guess is that there would not be a problem, but I do not know the diversity of the data.

@sheridancbio Hey Rob, any news on this one?

thomasyu888 commented 1 year ago

@ruslan-forostianov Apologies - I unfortunately haven't had the time to do a quick scan of all the input vcf files I get. Ill try to do that very soon.

sheridancbio commented 1 year ago

Just letting @ruslan-forostianov know that I'm still watching this PR. Maybe we can merge it and then revisit it if there are any downstream problems for @thomasyu888 ( I do think that it is unlikely to cause problems ) Would that be ok @thomasyu888 ?

thomasyu888 commented 1 year ago

That is ok with me @sheridancbio . Apologies I haven't had much bandwidth to explore.

sheridancbio commented 1 year ago

No worries. Thanks.