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 ------------------------------------------------------------------------------ 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
