Hi Hannes, sorry for misleading you. I believed it used to work, but trying with a few tabix versions, it does not. Unfortunately, at the moment I can't offer a solution other than clumsy piping through awk (awk '$2>=25'). We may want to add an option for this in bcftools and tabix, so that the user can control this behaviour.
Petr On Tue, 2015-05-19 at 14:46 +0200, Hannes Svardal wrote: > Hi Petr, > > > Thanks for the reply. > Strangely, I tried this but it gives me exactly the same result, i.e., > overlapping indels are again included even if the position is outside > the interval. > > > How can this be? Does tabix somehow detect that this is a VCF and > overrides the tabix -s 1 -b 2 -e 2 setting? > > > I do: > rm filename.vcf.gz.tbi > tabix -s 1 -b 2 -e 2 filename.vcf.gz > tabix filename.vcf.gz 'CAE1:25-45' > > > And get positions starting with CAE1 12 > > > Any ideas? > > > Thanks, > Hannes > > > > On 19 May 2015 at 14:34, Petr Danecek <[email protected]> wrote: > Hi Hannes, > > it does what you want and has no side effects other than that > the index > works by position only and does not take indels into account > > tabix -s 1 -b 2 -e 2 > > Petr > > On Mon, 2015-05-18 at 22:19 +0200, Hannes Svardal wrote: > > Hi, > > > > > > I have a vcf with all sites produced by GATK. > > I use bgzip to compress it and tabix 0.2.5 (r1005) to index > it. > > (tabix -p vcf filename.gz) > > > > > > When I retrieve a region I do not only get the entries in > this region > > but also all entries with a position smaller than the > desired start > > position if the entry represents a deletion and the length > of the > > reference allele reaches the desired start position. > > > > > > E.g. if I query for 'Chr1:25:45' > > > > > > Chr1 12 . AAAAAAAAACAAAAC A ... > > Chr1 19 . AACAAAAC A ... > > Chr1 20 . ACAAAAC A,AAAAAC ... > > Chr1 23 . AAAC A ... > > Chr1 25 . A . ... > > ... > > ... > > > > > > Is there a way to only get entries for which the pos (column > 2) is in > > the interval? > > > > > > I can imagine that the current behavior is sometimes > desired, but it > > is problematic in my case. The current behaviour means that > if I use > > tabix to split a VCF I will get duplicate entries on joining > it again. > > > > > > Could I just solve the problem by using tabix -s 1 -b 2 -e 2 > > <filename.gz>, or does -p vcf do anything more > sophisticated I should > > be aware of? > > > > > > Thanks for your help, > > Hannes > > > > > > > > > > > > > > -- > > Dr. Hannes Svardal > > Postdoctoral researcher > > Nordborg group > > > > Gregor Mendel Institute > > Dr. Bohr-Gasse 3 > > 1030 Vienna, Austria > > phone: +436803252197 > > > > > > > > > ------------------------------------------------------------------------------ > > One dashboard for servers and applications across > Physical-Virtual-Cloud > > Widest out-of-the-box monitoring support with 50+ > applications > > Performance metrics, stats and reports that give you > Actionable Insights > > Deep dive visibility with transaction tracing using APM > Insight. > > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > > _______________________________________________ > 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. > > -- 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. ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
