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From: Petr D. <pd...@sa...> - 2013-05-28 11:45:47
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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
>
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