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Re: [Vcftools-help] vcf-to-tab handling of unphased genotypes
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From: Heidi P. <hei...@gm...> - 2014-03-21 14:44:43
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Thanks so much, that's exactly what I needed! On Fri, Mar 21, 2014 at 4:51 AM, Petr Danecek <pd...@sa...> wrote: > Hi Heidi, > > please use vcf-query (or the newer version 'bcftools query') instead. > This tool can do what you want and much more: > > bcftools query -f'%REF %ALT [%TGT]\n' input.vcf > > http://vcftools.sourceforge.net/perl_module.html#vcf-query > http://samtools.github.io/bcftools/bcftools.html#query > > Petr > > > On Wed, 2014-03-19 at 09:46 -0400, Heidi Pagán wrote: > > Hi, I had a question about how unphased genotypes are treated by > > vcf-to-tab. > > > > > > If my input vcf file has the following: > > > > > > REF ALT GT > > > > G A 0/1 > > > > A C 1|0 > > > > C A 1|0 > > > > T A 1|0 > > > > C A 0|1 > > > > > > > > I find that the output does not reflect that the first variant > > genotype is unphased: > > > > > > G/A > > > > C/A > > > > A/C > > > > A/T > > > > C/A > > > > > > Is there any option for it to output some indication that the genotype > > is not phased at that position? > > > > > > Thank you, > > > > > > ~ Heidi > > > > > ------------------------------------------------------------------------------ > > Learn Graph Databases - Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases and > their > > applications. Written by three acclaimed leaders in the field, > > this first edition is now available. Download your free book today! > > http://p.sf.net/sfu/13534_NeoTech > > _______________________________________________ > > Vcftools-help mailing list > > Vcf...@li... > > https://lists.sourceforge.net/lists/listinfo/vcftools-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. > |
