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Vcf-Tools : Error "Broken Vcf Header, No Column Names?'"

I've indexed a set of vcf with tabix.

$ gunzip -c A.vcf.bgz 
##fileformat=VCFv4.1
(...)
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    A
chr1    10109    .    A    T    101.0    .    DP=101;VDB=0.0164;AF1=0.5;AC1=1;DP4=27,19,13,23;MQ=25;FQ=104;PV4=0.049,9.6e-06,0.056,0.15    GT:PL:GQ    0/1:131,0,233:99
chr1    10177    .    ACC    ACCC    70.5    .    INDEL;DP=56;VDB=0.0099;AF1=1;AC1=2;DP4=0,0,0,27;MQ=21;FQ=-116    GT:PL:GQ    1/1:111,81,0:99
chr1    10179    .    C    CN    70.5    .    INDEL;DP=59;VDB=0.0140;AF1=1;AC1=2;DP4=0,0,0,27;MQ=21;FQ=-116    GT:PL:GQ    1/1:111,81,0:99
chr1    10230    .    ACCCC    ACCC    9.02    .    INDEL;DP=50;VDB=0.0322;AF1=0.6672;AC1=1;DP4=0,2,0,8;MQ=20;FQ=-31.5;PV4=1,1,0.051,0.42    GT:PL:GQ    0/1:45,
0,3:7

$ tabix A.vcf.bgz chr1:10177-10178
chr1    10177    .    ACC    ACCC    70.5    .    INDEL;DP=56;VDB=0.0099;AF1=1;AC1=2;DP4=0,0,0,27;MQ=21;FQ=-116    GT:PL:GQ    1/1:111,81,0:99

tabix and vcf-tools/bin are in my $PATH

I've set PERL5LIB to /path/to/vcftools0.1.9/lib/perl5/siteperl

when I try to merge my VCFs with VCFtools I get the following error:

$ vcf-merge A.vcf.bgz B.vcf.bgz

Could not parse the fileformat version string [(#######large BINARY string###############)
], assuming VCFv4.1
Broken VCF header, no column names?
 at /usr/local/package/vcftools_0.1.9/lib/perl5/site_perl/Vcf.pm line 177
    Vcf::throw('Vcf4_1=HASH(0x1e04e200)', 'Broken VCF header, no column names?') called at /usr/local/package/vcftools_0.1.9/lib/perl5/site_perl/Vcf.pm line 868
    VcfReader::_read_column_names('Vcf4_1=HASH(0x1e04e200)') called at /usr/local/package/vcftools_0.1.9/lib/perl5/site_perl/Vcf.pm line 610
    VcfReader::parse_header('Vcf4_1=HASH(0x1e04e200)') called at /usr/local/package/vcftools_0.1.9/bin/vcf-merge line 168
    main::init_cols('HASH(0x1e3d73d0)', 'Vcf4_1=HASH(0x1e04dc20)') called at /usr/local/package/vcftools_0.1.9/bin/vcf-merge line 264
    main::merge_vcf_files('HASH(0x1e3d73d0)') called at /usr/local/package/vcftools_0.1.9/bin/vcf-merge line 12

what's wrong with my command ?

Pierre

vcftools vcf perl
• 13,627 views • link
updated by Anop Singh Ranawat • Anop Singh Ranawat • written by Pierre Lindenbaum Pierre Lindenbaum

I have the same problem as Pierre, just with a different tool. I also used bgzip, tabix and added the perlpath. Just my vcf file has a .gz and not a .bgz, but still I get the same error as Pierre. Any additional suggestions? Thanks Eva

• 0 views • link
written by eva.knig • eva.knig

Did you get any error messages while runing tabix? ; check if VCF is sorted or not? I generally follow this: for F in *.vcf ; do vcf-sort $F | bgzip -c > ${F}.gz ; tabix -p vcf ${F}.gz ; done

• 0 views • link
written by Rm Rm

Hi I have the similar errors. Have you sorted it out ?

Thank in advance

• 0 views • link
written by figo figo

You do realize this is a 2 year old post, right? And you're just pointing to a (not so wholesome) solution that you've written in a blog that is essentially the same as Brad's solution from two years ago. That's not really helpful.

• 0 views • link
written by Ram Ram

1 answer

It looks like VCFTools handles bgzipped/tabix files by recognizing a '.gz' extension. See line 209 of:

http://vcftools.svn.sourceforge.net/viewvc/vcftools/perl/Vcf.pm?revision=773&view=markup

So the bgz extension confuses it and results in trying to read your bgzipped input as plain text.

• 163 views • link
written by Brad Chapman Brad Chapman

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