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
