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Added a description and link to VCF File Management under curation
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carolyncaron committed Jan 2, 2024
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2 changes: 2 additions & 0 deletions _data/toc.yml
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children:
- title: "Genotypic Data Import"
url: "docs/curation/genotypic-data/genotypic-data-importer"
- title: "VCF File Management"
url: "docs/curation/genotypic-data/vcf-management"
- title: "Genetic Maps"
url: "docs/curation/genetic-maps"

5 changes: 4 additions & 1 deletion _docs/curation/genotypic-data.md
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This module package provides generic support for large-scale genotypic data, genetic maps, and QTL with importers, content pages and visualizations.

## [Genotypic Data Import](genotypic-data/genotypic-data-importer)
The genotypic data importer accommodates genotypic data stored in the VCF file format, as well as a more simplified matrix file format. These data, even large-scale datasets, are stored within Chado's relational database model with tight integration to germplasm and phenotypic data.
The genotypic data importer accommodates genotypic data stored in the variant call format (VCF), as well as a more simplified matrix file format. These data, even large-scale datasets, are stored within Chado's relational database model with tight integration to germplasm and phenotypic data.

## [VCF File Management](genotypic-data/vcf-management)
This functionality provides a means of uploading variant call format (VCF) files so that users can access pertinent metadata, filter and convert genotypic data to a format that suits their needs. This can be useful when a genotypic dataset is not ready for import into the database and multiple researchers will be using it for their projects. A researcher may also require access to the data in a specific format required by analysis software. The curator will have the ability to control user access, include the methods that generated the dataset, generate statistical summaries, and specify which conversions to other file formats are appropriate to that dataset.

7 changes: 7 additions & 0 deletions _docs/curation/genotypic-data/vcf-management.md
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---
title: VCF File Management
tags:
- genotype
- vcf
description: This is documentation pertaining to the curation of VCF files that are managed within TripalCultivate.
---

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