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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
211 stars 63 forks source link

Add support for viewing no_ref CRAM files #4644

Closed cmdcolin closed 2 weeks ago

cmdcolin commented 2 weeks ago

Initially reported here https://github.com/GMOD/jbrowse-components/issues/4637

My initial take was that no_ref was all bad and no good, but I did an additional analysis and found that in the no_ref case, samtools is actually adding an MD field to the CRAM file, and MD can be used to resolve SNPs

cmdcolin commented 2 weeks ago

See short analysis here https://github.com/galaxyproject/tools-iuc/issues/6523#issuecomment-2462927211