No, not right now. You have to do explicit counting. Heng
On Nov 21, 2014, at 15:34, Tommy Carstensen <t...@sanger.ac.uk> wrote: > Is it also possible to get the number of variants in a region > (chrom:pos1-pos2) of a vcf file with bcftools? > > On 19/11/2014 18:46, "Shane McCarthy" <s...@sanger.ac.uk> wrote: > >> If you have created your index with the htslib version of tabix or with >> bcftools index, then this will give you the total number of variants >> (bcftools v1.1): >> >> bcftools index --nrecords $vcf >> >> and this will give you counts per-chromosome: >> >> bcftools index --stats $vcf >> >> >> >> >> On 19 Nov 2014, at 16:15, Heng Li wrote: >> >>> >>> On Nov 19, 2014, at 10:58, Karol Estrada <ka...@broadinstitute.org> >>> wrote: >>> >>>> Dear Heng, >>>> >>>> We are wondering if there¹s a fast approach to use tabix or any other >>>> hack to get the total number of variants that a VCF has without >>>> actually reading the whole vcf file and counting the lines. I assume >>>> that the total number of rows is somehow stored in the tbi file. >>> >>> No, this is not stored in the traditional tabix index. The htslib >>> implementation of tabix should have this information in dummy bins, I >>> think. Someone else needs to confirm, though. >>> >>> Heng >>> >>> >>>> I read the spec of the tabix format, is n_ref the value we would be >>>> looking for? that doesn¹t seem to match the number of variants. >>>> >>>> Thanks >>>> >>>> Karol >>>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> ----- >>> 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=157005751&iu=/4140/ostg.clk >>> trk >>> _______________________________________________ >>> 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=157005751&iu=/4140/ostg.clkt >> rk >> _______________________________________________ >> 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=157005751&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ 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=157005751&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
