The documentation was about MAPQ scores, but regardless is the same as what I wrote (i.e., Phred or MAPQ + 33). The point in adding 33 (or a similar offset) to Phred and MAPQ scores is that they can then be represented by printable ASCII characters. If one were to subtract 33, that wouldn't work (in fact, you'd often get a negative value).
Devon ____________________________________________ Devon Ryan, Ph.D. Email: dpr...@dpryan.com 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 10:53 PM, Thiago M. Venancio wrote: > The documentation says the phred score minus 33 at > http://samtools.sourceforge.net/pileup.shtml > > Is that plus or minus 33 ? > > Thanks. > Thiago > > > On Mon, Aug 4, 2014 at 5:30 PM, Devon Ryan <dpr...@dpryan.com> wrote: > A dot means a match on the forward strand and a comma a match on the reverse > strand, so there's no difference (aka mismatch) in either read covering that > position. The last column is indeed Phred score + 33. > > FYI, if you were to input multiple BAM files, you'd find the output similar, > with some of the columns repeated for each of the samples. > > Devon > > ____________________________________________ > Devon Ryan, Ph.D. > Email: dpr...@dpryan.com > 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 10:21 PM, Thiago M. Venancio wrote: > > > 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 <dpr...@dpryan.com> 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: dpr...@dpryan.com > > 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 > > > ------------------------------------------------------------------------------ > > > Infragistics Professional > > > Build stunning WinForms apps today! > > > Reboot your WinForms applications with our WinForms controls. > > > Build a bridge from your legacy apps to the future. > > > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk_______________________________________________ > > > Samtools-help mailing list > > > Samtools-help@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > > > > > > > -- > > ================================= > > Thiago Motta Venancio, M.Sc., PhD > > http://venancio.openwetware.org/ > > ================================= > > > > > -- > ================================= > Thiago Motta Venancio, M.Sc., PhD > http://venancio.openwetware.org/ > ================================= ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
