Hello I encountered something strange. When I use:

samtools index sample.bam

I see no output, error message, or new file.

Then I tried it w/o the file name:

samtools index

I see something I expect to see:

Usage: samtools index [-bc] [-m INT] <in.bam> [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]

So what exact was the issue? I have not seen samtools index acting like this before. Any advice? Thank you so much!

=========

Updated 05/06/2017 Like advised in the comments, the issue was that I did not sort my input bam, which was generated by extracting one chromosome from a large sorted bam file. Apparently, I need to sort it again:

samtools sort sample.bam sample.sort
#Note samtools sort will add ".bam" extension to output automatically and therefore I did not add ".bam" to "sample.sort"

Then do

samtools index sample.sort.bam