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
> >
> >
> >
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