Update Documentation - Githubissues

Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF

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Update Documentation #1

Closed brcopeland closed 2 years ago

brcopeland commented 3 years ago

This should at a minimum include:

explaining the parameters one is prompted to enter
the QC features
expected output files

brcopeland commented 3 years ago

Also need to mention that when using FASTQs a read group text file is required.

brcopeland commented 3 years ago

Additionally no sample should be named joint, genomics_db (not that that would be likely in the first place).

brcopeland commented 2 years ago

I'm still working on the wiki but a lot of this is now available. Still need primarily to document the output files, but I'm going to go ahead and close this now.