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 there’s 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 doesn’t 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.clktrk > _______________________________________________ > 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
