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  • maubp
    replied
    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?

    Leave a comment:


  • kgulukota
    replied
    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).

    Leave a comment:


  • maubp
    replied
    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).

    Leave a comment:


  • kgulukota
    replied
    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 ...

    Leave a comment:


  • twaddlac
    replied
    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!

    Leave a comment:


  • kgulukota
    started a topic Why does samtools idxstats not show the stats

    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

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