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The GDC provides developers and users with a variety tools, components, and other key information in support of developing novel apps for visualizing and analyzing GDC data. The GDC Application Programming Interface (API) provides developers with a programmatic interface to query, analyze, and download GDC data and submit data to the GDC. The GDC Analysis Tool Software Development Kit supports the development of applications that allow for analysis, visualization, and refinement of cohorts. Applications that operate within the GDC Data Portal interact with the GDC API via SDK. The GDC provides a Component Library to facilitate the development of web-based applications for the GDC Data Portal. The GDC Data Model is the central method of organization of all data artifacts ingested by the GDC. |
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How can I download BAM index files (BAI files) using the API?
BAI files are included with the download when using the GDC Data Transfer Tool to download BAM files.
When using the API to download BAM files, BAI files will only be included if the related_files=true parameter is specified together with the BAM UUID, for example:
https://api.gdc.cancer.gov/data/53f4ad60-0777-409c-a34d-ca4442dc9c44?related_files=true
Alternatively, users can determine the BAI file UUID from the API files endpoint by supplying the BAM UUID. The BAI file UUID can then be used to download the BAI file from the data endpoint.
https://api.gdc.cancer.gov/files/53f4ad60-0777-409c-a34d-ca4442dc9c44?pretty=true&expand=index_files
https://api.gdc.cancer.gov/data/60cefd89-b428-46b7-b5b0-3b6e2743ab20
Note: BAI files are not available for sliced BAM files.
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