[tgolubch]

Thanks, Nils; I had already tried changing the prefix, but it still seems to fail -- I'll look into it again when I have time.

[Jeckow]

Hi nilshomer and thanks for your reply!

I've sorted and created the indexes but the samtools message remains the same.
Any other ideas? Do you know if there exists another way to extract a particular chromosomal region from a .bam file?
Thanks,

M.

[nilshomer]

Hi nilshomer and thanks for your reply!

I've sorted and created the indexes but the samtools message remains the same.
Any other ideas? Do you know if there exists another way to extract a particular chromosomal region from a .bam file?
Thanks,

M.

You could just run "samtools view in.bam | grep chr22" for example. Weird that your merge fails.

Nils

[nilshomer]

Thanks, Nils; I had already tried changing the prefix, but it still seems to fail -- I'll look into it again when I have time.

Could you post your example (with a download link) to [email protected] so I can take a look?

Nils

[Alberto Magi]

Hi all,

i need help to obtain read depth of coverage from a .bam file. Does anybody know some tool to automatically obtain a tab-delimited file (with chromosome, position, coverage depth.....) starting from a bam file?
i wait for suggestions
thanks a lot

Alberto

[apfejes]

That sounds suspiciously similar to a wig file, although, the format is not quite what you're expecting. I assume what you're looking for would look like:

chr1 1 0
chr2 2 1
chr2 3 1
... etc

The problem is that such file would be incredibly inefficient, hence the wig file, which will provide a more compact version. (Presumably the "variable width" format is what you're looking for.)

Although not quite the same, FindPeaks 4.0 (Yes, sorry, I'm plugging my own software) will generate fixedstep format wig files from sam/bam files, which would give you a similar result, which would look like:

fixedStep chrom=chr22 start=16653550 step=1
6
7
8
9
10
11
......

where you get a single line that tells you the start point (chr and position), and then the coverage of each position after that.

There are plenty of other wig file generators out there as well - although I'm not sure how many of them read bam/sam yet.

Cheers

[lh3]

@Alberto Magi

What you are looking for is "pileup" (http://samtools.sourceforge.net/pileup.shtml). Please also see this page (http://samtools.sourceforge.net/pipe.shtml) about getting pileup in a specified region.

@apfejes

Pileup output is not part of Picard, you should be able to get similar things from GATK (http://www.broadinstitute.org/gsa/wi...alysis_Toolkit)

[apfejes]

Thanks - pileup also fits that description. Variety is the spice of life. (=

Though, just to clarify, I was just looking to point Alberto in the right direction, and had forgotten about pileup. (I don't use pileup, but I do use Picard.)

[torrey]

I was curious if anyone has found a workaround to this error? It is coming up for me when viewing novoalign alignments. I am using samtools 0.1.6 (r453), and get the following error when loading a samtools converted bam file from novoalign's sam file

samtools: bam_lpileup.c:116: tview_func: Assertion `l == tv->n_pre' failed.


thanks

I was wondering if I could get some help on the SAM specification.

I get the error:



When I page the viewer to my reads containing indels. A sample of my data is



And I'm using novoalign format where I've modified the novo2sam.pl script to produce a 'correct' CIGAR format. Most samtools operation work except for the tview

[lh3]

Do you have a small sample file for me to test? Thanks.

[polivares]

http://seqanswers.com/forums/showthread.php?t=806

[wumblehoots]

Pileup Base Quality

Hi, I was wondering if anyone could point me in the direction of any documentation that describes how to interpret the base quality information reported within a pileup format file.

I've checked here: http://samtools.sourceforge.net/pileup.shtml but can't find any information.

Cheers

[houhuabin]

Hi heng,
I used samtools to built my bam file, but it dose't have a @HD field, which is needed by GATK's check for sort. How can I fix it?

[jasonbcold]

Sam/bam to jbrowse

Hi there,
does anyone know, how to use/upload alignments in sam/bam format to jbrowse?
thanks,
peter

[polivares]

@jasonbcold
I have not used jbrowse but I'd recommend you to try IGV which can load indexed BAM alignments without any trouble. If you need some helo PM me.