Re: [Vcftools-help] vcf-validator help

[Petr D. <pd...@sa...>]

Hi,

you file is not bgzipped and indexed with tabix. Please take a look at
the documentation, you'll find the answer there.
http://vcftools.sourceforge.net/perl_module.html

Best,
Petr


On Tue, 2011-10-25 at 11:24 +0530, Neeba Dijo wrote:
> HI the code you provide shows an error
> 
> 
> [tabix] was bgzip used to compress this file?
> HG00097_24.OCT.11.chr1.chr2.vcf
> [main] fail to load the index file.
> 
> 
> PLease help me 
> 
> 
> 2011/10/24 Petr Danecek <pd...@sa...>
>         In previous versions, the validator would print this error
>         message when
>         the VCF header block was repeated several times throughout the
>         file.
>         This has been fixed in recent SVN versions, a more informative
>         error
>         message is now printed.
>         
>         If that's the problem of your VCF file, you can fix it e.g. by
>         
>         (tabix -h broken.vcf.gz `tabix -l broken.vcf.gz | head -1`;
>         tabix -l broken.vcf.gz | tail -n +2 | while read CHR; do
>           tabix broken.vcf.gz $CHR;
>         done) | bgzip -c > out.vcf.gz
>         
>         Petr
>         
>         
>         
>         
>         On Mon, 2011-10-24 at 14:22 +0530, Neeba Dijo wrote:
>         > HI Guys,
>         >
>         >
>         > I am working with vcf-validator
>         >
>         >
>         > When validating the large files(2 GB) It shows error
>         >
>         >
>         > nsebastian@ip-10-0-14-69:/store/1319016987$ vcf-validator
>          HG00096.vcf
>         > FIXME: parse_header must be called before next_data_hash.
>         >
>         >
>         >  at /store/software/vcftools_0.1.6/perl/Vcf.pm line 169
>         >         Vcf::throw('Vcf4_0=HASH(0x20961b8)', 'FIXME:
>         parse_header must
>         > be called before next_data_hash.\x{a}') called
>         > at /store/software/vcftools_0.1.6/perl/Vcf.pm line 484
>         >         VcfReader::next_data_hash('Vcf4_0=HASH(0x20961b8)')
>         called
>         > at /store/software/vcftools_0.1.6/perl/Vcf.pm line 2045
>         >         VcfReader::run_validation('Vcf4_0=HASH(0x20961b8)')
>         called
>         > at /store/software/vcftools_0.1.6/bin/vcf-validator line 60
>         >         main::do_validation('HASH(0x1cfed48)') called
>         > at /store/software/vcftools_0.1.6/bin/vcf-validator line 14
>         >
>         >
>         >
>         >
>         > But if I validate a portionof the same  file with
>         vcf-validator  works
>         > correctly
>         >
>         >
>         > I any understand what is the problem please help me
>         >
>         >
>         >
>         >
>         
>         >
>         ------------------------------------------------------------------------------
>         > The demand for IT networking professionals continues to
>         grow, and the
>         > demand for specialized networking skills is growing even
>         more rapidly.
>         > Take a complimentary Learning@Cisco Self-Assessment and
>         learn
>         > about Cisco certifications, training, and career
>         opportunities.
>         > http://p.sf.net/sfu/cisco-dev2dev
>         > _______________________________________________
>         Vcftools-help mailing list Vcf...@li...
>         https://lists.sourceforge.net/lists/listinfo/vcftools-help
>         
>         
>         
>         
>         --
>          The Wellcome Trust Sanger Institute is operated by Genome
>         Research
>          Limited, a charity registered in England with number 1021457
>         and a
>          company registered in England with number 2742969, whose
>         registered
>          office is 215 Euston Road, London, NW1 2BE.
> 
> 




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.