mpileup is the first step in the calling process, QUAL is calculated by `bcftools call`.
Please see here http://www.htslib.org/workflow Petr On Tue, 2016-03-22 at 16:08 +0000, Adam Witney wrote: > Hi, > > I am upgrading samtools moving from v0.1.18 to v1.3, but now the QUAL column > in the VCF is always 0. > > This is my command: > > samtools mpileup -uvf ref.fna sample.bam > > do I have to add a switch to generate qual now? > > Thanks > > Adam > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 > _______________________________________________ > Samtools-help mailing list > [email protected] > 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. ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
