Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Sprint:Summer 7
Description
IGB can now open and display contents of CRAM files distributed by Nebula Genomics.
AL has a recently downloaded CRAM file from Nebula that would be great to use, but it's huge - around 84 Gb.
For this task, let's use a command line tool to extract the data for chromosome 1, the chromosome shows by default when it opens the latest human genome available in the browser - hg38.
Let's deploy the actual data file on RENCI hosting and add it as a new data set in IGB Quickload main.
Once it is there, we can then create a tutorial and also a video showing how to open and load the reads to look for or sanity-check polymorphisms. The tutorial ought to explain the soft clips and the SNPs - what they are and how to interpret them. The materials could also explain how to visually check some of the SNP calls on the Nebula Web site.
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