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