Update Documentation to Reflect SNV refactoring

[cansavvy]

Purpose/implementation Section

Main changes

• Revamped the whole README to reflect the refactoring of the SNV scripts.
• Got rid of the 00-setup.R and its being called in the bash script.

What GitHub issue does your pull request address?

#296

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• Does this make the analysis and it methods more clear?
• Would you feel confident in re-running this analysis by looking at this documentation?
• Is there anything in particular that is missing and should be documented more?
• Is there anywhere that should have a link to a source some place that doesn't currently have a link?

Results

No new results just updating the documentation

Reproducibility Checklist

These items were taken care of previously.

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

[jashapiro]

Looks pretty good! There are few places where I think more detail would be good, and a bit of repetitiveness that could be cleaned up, I think.

[jashapiro]

Looks good.