Document input and output of generateIndex

[zhuchcn]

Description

Improved documentation for input and output files of generateIndex

The link in vignette is also fixed.

Closes #

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• I have read the code review guidelines and the code review best practice on GitHub check-list.
• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• All test cases passed locally.

[lydiayliu]

Can you double check my minor updates to the doc?