```
samtools index
```

Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...
   or: samtools index [-bc] [-m INT] <in.bam> [out.index]
Options:
  -b, --bai            Generate BAI-format index for BAM files [default]
  -c, --csi            Generate CSI-format index for BAM files
  -m, --min-shift INT  Set minimum interval size for CSI indices to 2^INT [14]
  -M                   Interpret all filename arguments as files to be indexed
  -o, --output FILE    Write index to FILE [alternative to <out.index> in args]
  -@, --threads INT    Sets the number of threads [none]