correct header with samtools mpileup

Question

[storm1907]

Hello, Samtools Mpileup does not generate correct headers Have error, when piling several files in the folder with samtools mpileup -A -E -f $reference $INPATH/*.bam > piled. When trying to run downstream applications (and view header with samtools view), I get error like "fail to read the header of file.bam" Headers in my sam and bam files are correct

Anyone else has this problem? thank you :)

[Pierre Lindenbaum]

the output of samtools pileup is NOT a SAM/BAM format.

[ATpoint]

Do you try to see the output mpileup with samtools?

[storm1907]

they are ASCII text, with very long lines and no header

NC_045512.2     12      A       9       ^].^].^].^].^].^].^].^].^].     EEEEEEEEE
NC_045512.2     13      T       10      .........^].    DFFBFGFFF>
NC_045512.2     14      A       10      ..........      FFFFG>GFGD
NC_045512.2     15      C       10      ..........      8BFEFDEFFF

[ATpoint]

Yes of course, that is the mpileup format. What actually were you expecting?

[storm1907]

So I should not expect any header? OK, will try to check out, why my downstream tool is asking for it

Thanks!

[swbarnes2]

Pileup files have no header. Bam files absolutely do have headers. You don't run samtools view on a pileup file.