Dear lazyweb, here is the new menu for samtools index:
Usage: samtools index [-bc] [-m INT] [out.index]
Options:
-b Generate BAI-format index for BAM files [default]
-c Generate CSI-format index for BAM files
-m INT Set minimum interval size for CSI indices to 2^INT [14]
What is the CSI index compared to BAI? Should I better use it instead of the 'old' BAI index? What's the benefit?
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written
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Pierre Lindenbaum
It depends on how long your contigs/chromosomes are. The biggest benefit to CSI is that it supports indexing BAM files with contigs longer than 2^29-1 bases. At least in plants this isn't an uncommon requirement.
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written
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Devon Ryan
Neat answer.
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written
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Matt Shirley
CSI also allows to choose a compromise between the size of index and region query performance (the -m parameter). The less the interval size, the larger the index is, but for region queries less computational work is required, because the index is more fine-grained.
BAI is a special case of CSI, with some minor differences.
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written
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lomereiter
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