[ensembl-dev] Error using VCFTools

[Will McLaren]

Hi Nick,

I believe this tool has been developed by the 1000 Genomes project people -
I'd suggest contacting them at info at 1000genomes.org

Documentation for the script is here:
http://www.1000genomes.org/variation-pattern-finder

Regards

Will McLaren
Ensembl Variation


On 20 February 2013 11:11, Nick England <nickengland at gmail.com> wrote:

> Hello all,
>
> I hope this is the correct place to ask. I am trying to use the Variant
> Pattern Finder perl script (
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/variation_pattern_finder/version_1.0/variant_pattern_finder.pl)
> to analyse the 1000genome data. I am getting an error message when I run it.
>
> I am using a command like:
> perl variant_pattern_finder.pl -vcf
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz-sample_panel_file
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel
>
> I am using version 69 of the Ensemble API as this seems to be the version
> which 1000genome is using.
>
> and I get the error message:
>
> Wrong number of fieldsin
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz;
> expected 1101, got 937. The offending line was:
> (very long list of numbers)
> at /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 177
>         Vcf::throw('Vcf4_1=HASH(0x131fbd8)', 'Wrong number of fieldsin
> ftp://ftp.1000genomes.ebi.ac.uk/vol1...') called at
> /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 508
>         VcfReader::next_data_hash('Vcf4_1=HASH(0x131fbd8)') called at
> /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 3393
>         Vcf4_1::next_data_hash('Vcf4_1=HASH(0x131fbd8)') called at
> variant_pattern_finder.pl line 105
>
> The exact number seems to change,  eg if I re-run it I get "expected 1101,
> got 455" instead of "got 937".
>
> Any help would be appreciated!
>
> Thanks,
>
> Nick England
>
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