Project_Template

This is a template for a project repository that can be cloned/copied by the analysts and used to keep track of their projects. Including keeping track of data files, code used in the analysis process, and any relevant reference files or outputs. This text can be replaced with a short text outlining project.

Project Overview

Description

This is where analysist and other contributors can write up an abstract-like text describing the project. Consider regular abstracts are around 300 words, keep this section to that length. Short introduction, a brief overview of the methods, and anticipated results. In total 3-4 paragraphs should be included here, no need for references.

Contributors

• Franjo Ivankovic (@franjoim)
• Daniel Howringan (@howrigan)
• ...

Presentations and Publications

• Conference poster, presented by Franjo Ivankovic (@franjoim)
• Conference talk, presented by Daniel Howrigan (@howrigan)
• Published paper
• ...

Data Overview

Sample Data

Short description of sample data used in the project. Here is an example: 1,000 individuals genotyped on Illumina GSA_MD_v3 platform in 4 batches. DNA derived from blood. Avaliable phenotypes of interest include schizophrenia case/control status. Alternatively, biobanks can also be used, for example: AllOfUs controlled tier release version 7, including short-read sequencing data and mental health diagnosis codes. At the end, include path to data:

PATH: path/to/data

URL: link.to.data

Reference Data

Include reference data used for all steps of QC and analysis, and include their paths or links. For example:

1kG3 reference panel: path/to/ref/panel (PATH)

hg19 map files: link.to.map/files (URL)

Methods Overview

Proved a high-level methods overview for the project here. For example, data will be taken in and processed through a typical GWAS quality control. Then we will run GWAS for each ancestry group and meta-analyize the resulting summary statistics files.

Theory

If needed, theory behind project can be outlined in this section. LaTeX can be used to render mathematical expressions. For example:

$$\left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right)$$

Staging

Provide brief overview of staging process for data analysis. Including what platform was used and how (e.g. local machine, GoogleCloud project, or UGER). Include versions of all relevant software used after this description. Inlcude links to scripts used to access software if it makes sense to do so.

Installed/used software: Shapeit4, Impute5, plin1.96...

Quality control

Date started: 00/00/00

Date finished: 00/00/00

Provide brief overview of quality control in text, then create a step-wise list and link to revelant files/segmets where one can find the example of the code used to run this analysis.

Analysis 1

Date started: 00/00/00

Date finished: 00/00/00

Provide a brief overview of analysis 1 in text, then create a step-wise list if necessary, and link relevant script files/segments which include the code used to obtain the final output used in the analysis. You may also include steps from your analyses here as a way of having a to do list included in your project. Each issue/to-do item gets its own within repository numerical id, eg:

• Issue 1 #1
• Issue 2 #2

Analysis 2

Date started: 00/00/00

Date finished: 00/00/00

Provide a brief overview of analysis 2 in text, then create a step-wise list if necessary, and link relevant script files/segments which include the code used to obtain the final output used in the analysis.

...