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  • Why does samtools idxstats not show the stats

    The ref sequences in my bam file are 1, 2, ...

    idxstats reports get that 0 reads are mapped to each reference.

    Code:
    $ samtools idxstats MyBam.bam
    1	197195432	0	0
    10	129993255	0	0
    11	121843856	0	0
    And yet, the bam file is fine, I can see millions of reads mapped to each reference sequence (with samtools view) and I can run mpileup on it as well. Why would idxstats not work? Any ideas?

    Thanks,
    Gulu
    Kamalakar Gulukota,
    Director,
    Center for Bioinformatics and Computational Biology
    NorthShore University Health System, [email protected]

  • #2
    I'm not sure why it wouldn't work - I never had a problem with it before.

    If you're looking for a workaround you could so something like:
    Code:
    samtools view MyBam.bam | cut -f3 | sort | uniq -c
    Though this will omit the length of the reference.

    I hope this helps!

    Comment


    • #3
      Thank you twaddlac! Yes, I have been doing something like that. Unfortunately I have multiple files and each file has billions of lines and hence my server takes hours per file for this. I thought idxstats might have a fast way. Oh well ...
      Kamalakar Gulukota,
      Director,
      Center for Bioinformatics and Computational Biology
      NorthShore University Health System, [email protected]

      Comment


      • #4
        Try reindexing - 'samtools idxstats' relies on extra fields in the BAI file which are not present in very old BAI files (early versions of 'samtools index' didn't write them).

        Comment


        • #5
          Thank you maubp!

          I reindexed and it worked fine. (The original .bai file was something I downloaded from a public site along with the bam file).
          Kamalakar Gulukota,
          Director,
          Center for Bioinformatics and Computational Biology
          NorthShore University Health System, [email protected]

          Comment


          • #6
            Originally posted by kgulukota View Post
            Thank you maubp!

            I reindexed and it worked fine. (The original .bai file was something I downloaded from a public site along with the bam file).
            Great - can you try contacting the site so they can update their BAI files too?

            Comment

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