Re: [Vcftools-help] tabix

[Petr D. <pd...@sa...>]

Hi Hasani,

it looks as if you were at the same time trying to index (-f) and to
query the VCF. Please try first to index and then to run your query, in
two separate commands. Tabix will not do both in one go.

Petr


On Fri, 2013-05-24 at 17:55 +0200, Al-Hasani, Hoor wrote:
> Dear vcftools team,
> 
> I hope you kindly help me with a tabix problem (knowing it is not a
> vcftool) ...
> 
> I'm trying to extract CEU SNPs, after downloading ALL.chr
> ${i}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
> I'm using this command to index the file:
> 
> tabix -fh /work/.../1kG/ALL.chr
> ${i}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
> ${i}:1-$chrm_size > ALL.chr${i}.vcf
> 
> then to filter and extract the SNPs
> 
> vcftools --vcf ALL.chr${i}.vcf --plink-tped --keep CEU.samples.list
> --remove-indels --min-alleles 2 --max-alleles 2 --maf 0.01 --max-maf
> 0.99 --out chr${i}
> 
> before running any of these commands I made sure to add the tool's
> paths
> export PATH=${PATH}:/work/.../vcftools_0.1.9/bin
> export PATH=${PATH}:/work/.../vcftools_0.1.9/perl
> export PERL5LIB=/work/.../vcftools_0.1.9/perl:$PERL5LIB
> export PATH=${PATH}:/work/.../tabix-0.2.6/
> 
> However, I'm getting the error [tabix] failed to load the index file
> The strange thing, if I tried it like this
> tabix -fh
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr
> ${i}.phase... I don't get any error.
> 
> Could you please help? I already lost time on trying over and over
> (same paths, complete paths, no paths, different parameters...)
> 
> Thank you very much in advance!
> 
> Hasani
> 
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service 
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may
> _______________________________________________
> Vcftools-help mailing list
> Vcf...@li...
> https://lists.sourceforge.net/lists/listinfo/vcftools-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.