Hi Thiago, this was a limitations of previous versions of samtools. If you upgrade to the latest version and run `bcftools call -m`, non-reference heterozygous genotypes should appear correctly on the ouput as, e.g. 1/2.
Best Petr On Tue, 2014-08-05 at 13:25 -0300, Thiago M. Venancio wrote: > Hi all, > > > How does the VCF output handles multiple ALT alleles ? Some tutorials > I read say that: > > > ALT the alternate allele expressed as a sequence of one or more > A/C/G/T nucleotides (e.g. "A" or "AAC"). If there is more than one > alternate alleles, the field should be a comma-separated list of > alternate alleles. > > > > The most common format subfield is GT (genotype) data. If the GT > subfield is present, it must be the first subfield. In the sample > data, genotype alleles are numeric: the REF allele is 0, the first ALT > allele is 1, and so on. > > > > However, the GT fields in my results only have 0 and 1, even in the > multi-ALTs cases. How can I distinguish between the ALT alleles ? > > > One example: > supercontig_0 762229 . A G,T 123 . > DP=6;VDB=0.0045;AF1=1;AC1=4;DP4=0,0,3,3;MQ=42;FQ=-35.6 > GT:PL:DP:SP:GQ 1/1:62,6,0,62,6,62:2:0:15 > 1/1:101,14,5,93,0,90:4:0:18 > > > > I compared two individuals with a reference genome. I would expect at > least one number 2 in the last two columns. > > > Best, > Thiago > > > -- > ================================= > 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 > [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. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
