Question: vcfbreakmulti Broken VCF header, no column names?
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gravatar for vpnfatrsqlbahzpchbvi
19 months ago by
vpnfatrsqlbahzpchbvi0 wrote:

I'm trying to use vcfbreakmulti on some vcf file:

vcfbreakmulti fileIN.vcf > fileOUT.vcf

I'm getting:

Broken VCF header, no column names?
 at /home/krzysiek/Programy/vcftools-vcftools-1d27c24/src/perl/Vcf.pm line 172
        Vcf::throw('Vcf4_2=HASH(0x2074ef8)', 'Broken VCF header, no column names?') called at /home/vcftools/src/perl/Vcf.pm line 867

My vcftools version is 0.1.15. fileIN.vcf is vcf version 4.1.

grep "#CHROM" fileIN.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sampleName

Any ideas?

Edit: I've traced the error, it was not related to vcfbreakmulti. I was running it together with vcf-annotate in a pipe and vcf-annotate was trying to save to the same file as it was reading. Thanks everybody for suggestions.

vcftools • 1.0k views
ADD COMMENTlink modified 19 months ago • written 19 months ago by vpnfatrsqlbahzpchbvi0

please, show us

head -n1 fileIN.vcf

and

grep -B 5 "#CHROM" fileIN.vcf
ADD REPLYlink modified 19 months ago • written 19 months ago by Pierre Lindenbaum116k

head -n1 fileIN.vcf

##fileformat=VCFv4.1

grep -B 5 "#CHROM" fileIN.vcf

##INFO=<ID=OPOS,Number=.,Type=Integer,Description="List of original allele positions">
##INFO=<ID=OREF,Number=.,Type=String,Description="List of original reference bases">
##INFO=<ID=OALT,Number=.,Type=String,Description="List of original variant bases">
##INFO=<ID=OMAPALT,Number=.,Type=String,Description="Maps OID,OPOS,OREF,OALT entries to specific ALT alleles">
##deamination_metric=0.162637
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sampleName
ADD REPLYlink written 19 months ago by vpnfatrsqlbahzpchbvi0

One suggestion would be to use vcf-validator from vcftools to check for any specific issues with the vcf.

ADD REPLYlink written 19 months ago by microfuge970
 vcf-validator fileIN.vcf
    The header tag 'contig' not present for CHROM=chr1. (Not required but highly recommended.)
    The header tag 'contig' not present for CHROM=chr2. (Not required but highly recommended.)
    The header tag 'contig' not present for CHROM=chr3. (Not required but highly recommended.)
...
    The header tag 'contig' not present for CHROM=chr21. (Not required but highly recommended.)
    The header tag 'contig' not present for CHROM=chr22. (Not required but highly recommended.)
    The header tag 'contig' not present for CHROM=chrX. (Not required but highly recommended.)

I've got the same results for files that are working with vcfbreakmulti with no problem.

ADD REPLYlink written 19 months ago by vpnfatrsqlbahzpchbvi0
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