epam / epam/fonda

Snpsift tool references in the documentation

Open
#145 0 comments 0 reactions 0 assignees View on GitHub
documentation heritage
Dominant language
Java
Stars
8
Forks
2
PR merge metrics
No merged PRs in 30d

Description

**Background**

In the original Fonda documentation, the `snpsift` tool is stated in the toolset as an annotation tool. However, Fonda code does not check the tool is specified anywhere and performs `snpsift` annotation in the `vcf_snpeff_annotation.py` file. Perhaps it was originally envisaged for the other, but it was not implemented? If not, in order not to mislead the user, we suggest removing such examples in the documentation.

**Approach**

Remove `snpsift` tool references in the Fonda documentation.

Contributor guide

Open the contributing guide

Research direction

Search the Fonda documentation for `snpsift` references; the issue does not name specific documentation files. Remove the references described in the approach, then review the documentation to confirm that misleading `snpsift` examples no longer remain.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
55/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.