I'm trying to use vcfbreakmulti on some vcf file:
vcfbreakmulti fileIN.vcf > fileOUT.vcf
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
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.