Re: [Samtools-help] no header in BAM with -h

[Sean D. <sd...@ma...>]

The output is to stderr, not stdout.  You can use "top" in another shell to
see if samtools is still working or you can watch the filesize of the output
file to track progress.

Sean
On May 21, 2011 11:01 AM, "Dongsheng LU" <don...@gm...> wrote:
> Sorry for that mail because of my carelessness. If I use this command,
> $ samtools view -h unsorted.bam
> (unsorted.bam is the output of sam -> bam conversion)
> Then I can see the header in unsorted.bam.
>
>
> Could you please do me a favor to take a look at the problem as follows?
Anyway, if your time is available.
>
> When I tried to call variants by 25 BAM files like this, (The *.bam have
been all sorted and indexed.)
> $ samtools mpileup -P ILLUMINA -ugf hg19.fasta *.bam | bcftools view -bcvg
- > var.raw.bcf ; bcftools view var.raw.bcf | vcfutils.pl<http://vcfutils.pl>
varFilter -D 2000 > var.flt.vcf
>
>
> Then the standard output was
> [mpileup] 25 samples in 25 input files
> <mpileup> Set max per-file depth to 320
> [afs] 0:0.000 1:0.000 2:0.000 3:0.000 4:0.000 5:0.000 6:0.000 7:0.000
8:0.000 9:0.000 10:0.000 11:0.000 12:0.000 13:0.000 14:0.000 15:0.000
16:0.000 17:0.000 18:0.000 19:0.000 20:0.000 21:0.000 22:0.000 23:0.000
24:0.000 25:0.000 26:0.000 27:0.000 28:0.000 29:0.000 30:0.000 31:0.000
32:0.000 33:0.000 34:0.000 35:0.000 36:0.000 37:0.000 38:0.000 39:0.000
40:0.000 41:0.000 42:0.000 43:0.000 44:0.000 45:0.000 46:0.000 47:0.000
48:0.000 49:0.000 50:0.000
>
> then the samtools just stopped, I don't know why. Maybe you can give me
some suggestions about how to solve this question. Thank you very much.
>
> Best wishes.
>
> On Sat, May 21, 2011 at 10:25 PM, Sean Davis <sd...@ma...<mailto:
sd...@ma...>> wrote:
>
>
> On Thu, May 19, 2011 at 1:48 AM, Dongsheng LU <don...@gm...
<mailto:don...@gm...>> wrote:
> Hi,
>
> This is the command to convert sam to bam,
> $ samtools view -hbt hg19.fa.fai unsort.sam -o unsort.bam
>
> But there's no header in BAM file. Meanwhile, if I change the order for
parameters, for example
> $ samtools view -bth hg10.fa.fai unsort.sam -o unsort.bam
> the output will be
> [main_samview] fail to open "hg19.fa.fai" for reading
>
>
> Looks like hg19.fa.fai is not available. Is it in the directory?
>
> Sean
>
>
>
>
> --
>
*****************************************************************************
> Dongsheng LU
> Population Genomics Group (PGG)
> CAS-MPG Partner Institute for Computational Biology (PICB)
> Shanghai Institutes for Biological Sciences (SIBS)
> Chinese Academy of Sciences (CAS)
>
> 320 Yue Yang Rd.
> Shanghai, P.R. China 200031
>
> TEL: +86-21-5492-0463
> Email: lud...@pi...<mailto:lud...@pi...>
>
*****************************************************************************
>