Hi Jeanne, the VCF header says that INFO/DP="Raw read depth" and INFO/DP4="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases".
Does this answer your question? Best, petr On Tue, 2014-12-09 at 23:31 -0500, Jeanne Ropars wrote: > Hi, > > I wanted to know if there is a way to have the exact counts of reads > supporting the reference and alternate alleles because that's weird, > the reference alleles can be tagged 0 ! > Here is an example of my file : > > scaffold16|size214105 154542 . A G 487 . > DP=72;VDB=0.5037;SGB=27.7261;MQSB=0.972745;MQ0F=0;AC=4;AN=4;DP4=0,0,33,31;MQ=58 > GT:PL ./.:0,0,0 1/1:255,57,0 > 1/1:255,135,0 > scaffold16|size214105 168573 . T C 487 . > DP=75;VDB=0.347592;SGB=32.578;MQSB=0.890283;MQ0F=0;AC=4;AN=4;DP4=0,0,30,43;MQ=59 > GT:PL ./.:0,0,0 1/1:255, > 63,0 1/1:255,157,0 > > I would like to have the sum of my 4 columns of DP4 = DP, is it a way > to do that ? > > Thanks, > Jeanne > > > > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > _______________________________________________ Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
