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LincolnSteinLab / gdc-viewer

A JBrowse plugin for viewing GDC Data
https://lincolnsteinlab.github.io/gdc-viewer/
MIT License
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Investigate the GDC BAM Slicing API #82

Closed agduncan94 closed 3 years ago

agduncan94 commented 3 years ago

The GDC API supports BAM slicing (https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/)

Unfortunately, it doesn't provide an index file, so we would need to have the user generate this.

Try using the BAM slicing API to slice a BAM file. Then use samtools index to create an index and try using the alignment track to display.

GFJHogue commented 3 years ago

We found that the GDC API does provide index files for BAMs. Therefore this investigation is not needed.