Mitch -
Tabix helpfully returns all records which overlap any part of the query
region. So, some post-filtering on variant type is usually a good idea.
We all deal with this. Yes, sometimes you find out more than you really
wanted to know, but on balance it's better to see the other records than
not. Just be glad that the alternate allele for a 100 kb duplication is
no longer shown as a literal string !
- tom blackwell -
On Tue, 7 Oct 2014, Machiela, Mitchell (NIH/NCI) [F] wrote:
> Hi Samtools Help,
>
> I would like to pull genotypes for a single SNP from a 1000 Genomes VCF file
> for use in a larger pipeline. Rather than getting results for only the
> queried coordinates of my SNP, Tabix returns a record for my SNP as well as
> for other random variants outside the queried region. These variants are
> nearby my SNP of interest (rs6497270), but are not within the coordinates I
> specified. I am using the below command on Tabix 0.2.5 (r1005):
>
> tabix -fh
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz
> 15:28361040-28361040 > test.vcf
>
>
> The test.vcf file has results for these three variants:
>
> 15 28343591 DUP_uwash_chr15_28343591_28439869
>
> 15 28353161 DUP_gs_CNV_15_28353161_28366578
>
> 15 28361040 rs6497270
>
> Is this an error in Tabix, or is there a more precise Tabix command syntax I
> should be using to only pull information for one variant of interest? Any
> help you could give on this error would be of great assistance. Thanks!
>
> Mitch
>
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