Question: samtools 1.0 'index' : CSI index vs BAI index ?
gravatar for Pierre Lindenbaum
3.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum105k wrote:

Dear lazyweb, here is the new menu for 'samtools index':

Usage: samtools index [-bc] [-m INT]  [out.index]
  -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 ?

index samtools • 2.3k views
ADD COMMENTlink modified 3.5 years ago by lomereiter410 • written 3.5 years ago by Pierre Lindenbaum105k
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan76k
Freiburg, Germany
Devon Ryan76k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Devon Ryan76k

Neat answer.

ADD REPLYlink written 3.5 years ago by Matt Shirley8.2k
gravatar for lomereiter
3.5 years ago by
Russian Federation
lomereiter410 wrote:

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.

ADD COMMENTlink written 3.5 years ago by lomereiter410
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