No output from samtools index?

Question

[DVA]

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!

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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

[Devon Ryan]

After you samtools index sample.bam, try echo $?, which will return the number that samtools exited with. My guess is that it's not 0 (though I don't really know that it sets an appropriate exit code in all cases).

[DVA]

Thanks for the suggestions.

Answer 1

[GenoMax]

Have you sorted the BAM file?

[DVA]

Thank you it was indeed the issue. My input bam resulted from extraction of one chromosome of a sorted large bam. I thought the sorting was no longer needed.

[WouterDeCoster]

.toggled status to accepted.