index.Rmd

---
title: "MUGA Reference Genotypes"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: false
editor_options:
  chunk_output_type: console
---

## MUGA Genotype Data for Reference Samples and CC/DO Founder Strains

| File Name                                   | Description                                                                                  | Link  |
|---------------------------------------------|----------------------------------------------------------------------------------------------|-------|
| **MUGA_sample_metadata.csv**                | Metadata for samples passing QC from reference strains (sample name, sex, strain)            | [TBD] |
| **MUGA_founder_metadata.csv**               | Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) | [TBD] |
| **MUGA_genotypes.csv.gz**                   | Genotypes for markers passing QC from reference samples                                      | [TBD] |
| **MUGA_x\_intensities.csv.gz**              | Probe x-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **MUGA_y\_intensities.csv.gz**              | Probe y-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **MUGA_founder_consensus_genotypes.csv.gz** | CC/DO founder strain consensus genotypes for markers passing QC                              | [TBD] |
| **MUGA_founder_mean_x\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC       | [TBD] |
| **MUGA_founder_mean_y\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC       | [TBD] |

## MegaMUGA Genotype Data for Reference Samples and CC/DO Founder Strains

| File Name                                       | Description                                                                                  | Link  |
|-------------------------------------------------|----------------------------------------------------------------------------------------------|-------|
| **MegaMUGA_sample_metadata.csv**                | Metadata for samples passing QC from reference strains (sample name, sex, strain)            | [TBD] |
| **MegaMUGA_founder_metadata.csv**               | Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) | [TBD] |
| **MegaMUGA_genotypes.csv.gz**                   | Genotypes for markers passing QC from reference samples                                      | [TBD] |
| **MegaMUGA_x\_intensities.csv.gz**              | Probe x-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **MegaMUGA_y\_intensities.csv.gz**              | Probe y-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **MegaMUGA_founder_consensus_genotypes.csv.gz** | CC/DO founder strain consensus genotypes for markers passing QC                              | [TBD] |
| **MegaMUGA_founder_mean_x\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC       | [TBD] |
| **MegaMUGA_founder_mean_y\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC       | [TBD] |

## GigaMUGA Genotype Data for Reference Samples and CC/DO Founder Strains

| File Name                                       | Description                                                                                  | Link  |
|-------------------------------------------------|----------------------------------------------------------------------------------------------|-------|
| **GigaMUGA_sample_metadata.csv**                | Metadata for samples passing QC from reference strains (sample name, sex, strain)            | [TBD] |
| **GigaMUGA_founder_metadata.csv**               | Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) | [TBD] |
| **GigaMUGA_genotypes.csv.gz**                   | Genotypes for markers passing QC from reference samples                                      | [TBD] |
| **GigaMUGA_x\_intensities.csv.gz**              | Probe x-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **GigaMUGA_y\_intensities.csv.gz**              | Probe y-channel intensities from markers passing QC from reference samples                   | [TBD] |
| **GigaMUGA_founder_consensus_genotypes.csv.gz** | CC/DO founder strain consensus genotypes for markers passing QC                              | [TBD] |
| **GigaMUGA_founder_mean_x\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC       | [TBD] |
| **GigaMUGA_founder_mean_y\_intensities.csv.gz** | CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC       | [TBD] |