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cropgeeks / tablet

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
https://ics.hutton.ac.uk/tablet
BSD 2-Clause "Simplified" License
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Tablet does not support BAM files with CSI index, only BAI index #3

Open peterjc opened 6 years ago

peterjc commented 6 years ago

Resurrecting an old issue for the GitHub issue tracker,

The original BAM index format (BAI) has a fixed bin size system, and suffers from a maximum reference sequence length of 512Mbp making it unsuitable for large chromosomes (e.g. many plants, some marsupials).

The newer CSI indexing format supports longer references, and smaller bin sizes - which ought to help with ultra-high coverage in RNA sequencing or viral samples where currently Tablet can struggle and run out of RAM.

Testing with samtools 1.3, e.g. samtools index -c -m 5 example.bam, gives an index file example.bam.csi but Tablet does not recognise this.

Needs support in htslib https://github.com/samtools/htsjdk/issues/447

The htslib issue is still open, so I assume that has not yet been implemented.