[ensembl-dev] Error using VCFTools

[Nick England]

Dear future person who gets the same error I had,

I thought people might like to know after asking on the 1000genome address
that the problem was down to attempting to analyse too large a segment of
genome at once, which apparently causes a bug in Tabix which results in the
variable error message about expected data.

Using a smaller set of data at a time solves the problem.

Thanks,

Nick

On 20 February 2013 11:24, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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