lc-WGS repository and data available for assistance on summarizing oly pop gen data

[zbengt]

Issue Category

Please select the category that best describes your issue:

• [ ] Server/Infrastructure (Raven, Klone, Gannet connectivity, performance, or storage issues)
• [x] Bioinformatics Tools (Tool installation, container setup, pipeline errors, workflow issues)
• [ ] R/RStudio (Package installation, server connectivity, environment configuration)
• [x] Data Management (File transfers, storage, backup procedures, data organization)
• [ ] Access Management (Account requests, permissions, authentication setup)
• [ ] Lab Meeting Topic (Suggestions for lab meeting presentations or discussions)
• [ ] Equipment/Hardware (Lab equipment issues, hardware problems)
• [x] Other (Please describe in the issue description)

Computer System Information

Please provide details about the system you're working on:

Primary system (check all that apply):

• [x] Raven (lab server)
• [x] Klone (UW HPC cluster)
• [ ] Gannet (lab server)
• [ ] Personal computer (Mac/Windows/Linux)
• [ ] Other lab computer: ________________

Operating System (if known):

• [ ] Ubuntu/Linux
• [ ] macOS
• [ ] Windows
• [ ] Other: ________________

Connection method (if applicable):

• [ ] SSH/Terminal
• [x] RStudio Server
• [ ] VPN
• [ ] Direct connection
• [ ] Other: ________________

Issue Description

Please provide a clear description of your issue or request:

This issue is primarily for @sr320 to help me summarize pop gen information from my oly low-coverage WGS data. I have sent an invite to collaborate on my repo (https://github.com/zbengt/oly-lc-WGS) and the data is linked on the wiki (https://github.com/zbengt/oly-lc-WGS/wiki/Low%E2%80%90Coverage-WGS-Data). We previously discussed getting simple summary information from data to provide to Julieta by next Thursday (11/21).

Data includes unique sample IDs within file names. The ~100 samples are from 3 separate populations of Olympia oysters in the Puget Sound (North, Central, and South Sound locations).

Error Messages

If you encountered any error messages, please paste them here (use code blocks with triple backticks ```):

N/A

What You've Tried

Please describe any troubleshooting steps or solutions you've already attempted:

Have not completed any work with this data thus far other than grabbing data from basespace and hosting in nightingales.

Expected Outcome

What were you trying to accomplish or what result were you expecting?

Simple summary information from data to provide to Julieta by next Thursday (11/21)

Additional Context

Please provide any additional information that might be helpful:

• Relevant files or links: Repo (https://github.com/zbengt/oly-lc-WGS) and data (https://owl.fish.washington.edu/nightingales/O_lurida/lc-WGS_Aug2025/)
• Timeline/urgency: Ideally by 11/20
• Related issues:
• Screenshots (if applicable):