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 ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
