Details
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Type: New Feature
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Status: To-Do (View Workflow)
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Priority: Major
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Resolution: Unresolved
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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:3
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Epic Link:
Description
Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.
There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation.
See: https://www.biostars.org/p/111984/
For this new feature, enable IGB to support partial data loading of files indexed using tabix -C (which creates a .csi index instead of a .tbi index).
See attached for example BED file with csi index.
Attachments
Issue Links
Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-1765 [ 17855 ] |
Ann Loraine
made changes -
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Attachment | T_aestivum_Aug_2018.bed.gz [ 14874 ] | |
Attachment | T_aestivum_Aug_2018.bed.gz.csi [ 14875 ] |
Ann Loraine
made changes -
Description |
Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.
There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation. See: https://www.biostars.org/p/111984/ For this new feature, enable IGB to support partial data loading of files indexed using tabix with the -C option. See attached for example BED file with csi index. |
Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.
There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation. See: https://www.biostars.org/p/111984/ For this new feature, enable IGB to support partial data loading of files indexed using tabix -C (which creates a .csi index instead of a .tbi index). See attached for example BED file with csi index. |
Ann Loraine
made changes -
Summary | Support CSI index for BAM and bgzip (tabix) files | Support CSI index for tabix-indexed files |
Ann Loraine
made changes -
Sprint | Fall 2: 28 Sep - 9 Oct [ 104 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Ann Loraine
made changes -
Ann Loraine
made changes -
Summary | Support CSI index for tabix-indexed files | Support CSI tabix index for very large genomes |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Rank | Ranked lower |