Hi Devon and TNP,
Thanks for the feedback. Please allow me one clarification to see if I
understood the documentation correctly.
Thanke the following row from my example:
supercontig_0 32 C 2 ., BH
This means that at supercontig_0 we have a reference C at position 32, with
two mapped reads with potential SNPs. However, dot and comman means
differences between reads and each strand of the reference sequence. So, if
the sequencing method is not strand specific, these SNPs should be
excluded. Am I missing something or this point is correct ?
Finally, how the last column (base quality) should be interpreted ? Should
I use the ASCII of the character minus 33 ?
Sorry if these questions are very basic. I am just trying to make sure I
understood the process.
Best,
Thiago
On Mon, Aug 4, 2014 at 5:00 PM, Devon Ryan <[email protected]> wrote:
> Hi Thiagp
>
> The format, including the last 3 columns is described here:
> http://samtools.sourceforge.net/pileup.shtml
>
> Best,
> Devon
>
> ____________________________________________
> Devon Ryan, Ph.D.
> Email: [email protected]
> Tel: +49 (0)178 298-6067
> Molecular and Cellular Cognition Lab
> German Centre for Neurodegenerative Diseases (DZNE)
> Ludwig-Erhard-Allee 2
> 53175 Bonn, Germany
>
> On Aug 4, 2014, at 9:48 PM, Thiago M. Venancio wrote:
>
> > Hi all,
> >
> > I ran the samtools mpileup on a set of mapped reads (in bam format). The
> output gave me something like that:
> >
> > supercontig_0 30 T 2 ^g.^g, BH
> > supercontig_0 31 G 2 ., AG
> > supercontig_0 32 C 2 ., BH
> > supercontig_0 1689 T 4 .,^g.^g, GBA5
> > supercontig_0 1690 A 4 .,., GBAD
> > supercontig_0 1691 A 4 .,., BAAF
> > supercontig_0 1692 C 4 .$,$., EA?C
> >
> > I inspected all the documentation I could find over the past few hours
> and was unable to find a complete explanation for this output. I
> understand the first three columns, but not the other three.
> >
> > Can anyone point me the appropriate documentation ?
> >
> > Thanks in advance.
> > Thiago
> >
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--
=================================
Thiago Motta Venancio, M.Sc., PhD
http://venancio.openwetware.org/
=================================
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