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From: Petr D. <pd...@sa...> - 2011-10-25 07:41:29
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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. |