2024 analysis of WGSPD cohort
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.
- Conference poster, presented by Franjo Ivankovic (@franjoim)
- Conference talk, presented by Daniel Howrigan (@howrigan)
- Published paper
- ...
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
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)
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...
Date started: 202403
Date finished: 202404
WGSPD subset pulled from gnomadv3 genomes VDS. See subsetting/ for more details.
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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.
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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 Nealelab/Project_Template#1
- Issue 2 Nealelab/Project_Template#2
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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.
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