This is a test version of Biostars. For the public version, visit https://www.biostars.org.
correct header with samtools mpileup

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 :)

assembly
• 1,700 views • link
written by storm1907 • storm1907

Do you try to see the output mpileup with samtools?

• 0 views • link
written by ATpoint ATpoint

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
• 0 views • link
written by storm1907 • storm1907

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

• 0 views • link
written by ATpoint ATpoint

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

Thanks!

• 0 views • link
written by storm1907 • storm1907

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

• 0 views • link
written by swbarnes2 swbarnes2

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

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

0 answers

No answers yet.

Log in to answer this question.

More posts like this