Question: samtools 1.0 'index' : CSI index vs BAI index ?
2
gravatar for Pierre Lindenbaum
3.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum102k wrote:

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 ?

index samtools • 2.1k views
ADD COMMENTlink modified 3.3 years ago by lomereiter410 • written 3.3 years ago by Pierre Lindenbaum102k
6
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k 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 3.3 years ago by Devon Ryan74k
1

Neat answer.

ADD REPLYlink written 3.3 years ago by Matt Shirley8.0k
4
gravatar for lomereiter
3.3 years ago by
lomereiter410
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 3.3 years ago by lomereiter410
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