Why does samtools idxstats not show the stats

[kgulukota]

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

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

$ 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

[twaddlac]

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:

samtools view MyBam.bam | cut -f3 | sort | uniq -c

Though this will omit the length of the reference.

I hope this helps!

[kgulukota]

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 ...

[maubp]

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).

[kgulukota]

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).

[maubp]

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?