How to use the json file with IGV, Biodiance, JBrowse

hammerlab / bai-indexer

Build an index for your BAM Index (BAI)

Apache License 2.0

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How to use the json file with IGV, Biodiance, JBrowse #3

Open billzt opened 8 years ago

billzt commented 8 years ago

Well, the tool is really wonderful. But after I get the JSON file, how to use it with genome browsers such as IGV, Biodiance, JBrowse?

cmdcolin commented 6 years ago

Not sure if this is relevant but it seems like CSI and CRAI indexes are much smaller than BAI so could be alternatives (jbrowse supports these in v1.15.0)

danvk commented 6 years ago

For biodalliance, see https://github.com/dasmoth/dalliance/pull/121 For pileup.js, you specify it in your BamSpec: https://github.com/hammerlab/pileup.js/blob/893495424f56f33e27f8aeb8b93f1dd441afb847/src/main/sources/BamDataSource.js#L118