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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 BAM files from the GDC #79

Closed agduncan94 closed 4 years ago

agduncan94 commented 4 years ago

Investigate whether BAM files downloaded from the GDC portal work with the alignment track type.

There are two parts to this. 1) Download a BAM file and generate the index file locally. Using these two files, create an alignment track. Does this work? 2) Find a BAM file with an existing index. Set the URLtemplate path of an alignment track (and index path) to these locations (requires using the authentication token)

Use samtools index to generate the index file. See here.

Post your results to the investigation as a comment here.

agduncan94 commented 4 years ago

The GDC API has the concept of related files, which might be relevant for finding associated index files. https://docs.gdc.cancer.gov/API/Users_Guide/Downloading_Files/#related-files

GFJHogue commented 4 years ago
  1. Download a BAM file and generate the index file locally. Using these two files, create an alignment track. Does this work?

Confirmed that this works as stated. Downloaded a BAM, unzipped with tar -xf, generated the index with samtools index, and created an alignment track.

GFJHogue commented 4 years ago

Demonstrated adding a BAM track via URL with authentication token in #98