[ensembl-dev] Error using VCFTools

[Nick England]

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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