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ERROR MESSAGE: Your input file has a malformed header

ywy25ywy25 Member
edited June 2014 in Ask the GATK team

Dear GATK team,

I have got an error message while using RealignTargetCreator -- ERROR MESSAGE: Your input file has a malformed header: there are not enough columns present in the header line: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
However, after checked the standard VCF format, I found it seems that there is no problem with my VCF file.

The VCF file is generated by Dindel. That would be great if you could told me why I got this error message.
Many thanks!

Here is the header and sample line:

##fileformat=VCFv4.0
##source=Dindel
##reference=ref.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total number of reads in haplotype window">
##INFO=<ID=HP,Number=1,Type=Integer,Description="Reference homopolymer tract length">
##INFO=<ID=NF,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on forward strand">
##INFO=<ID=NR,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on reverse strand">
##INFO=<ID=NFS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on forward strand">
##INFO=<ID=NRS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on reverse strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##ALT=<ID=DEL,Description="Deletion">
##FILTER=<ID=q20,Description="Quality below 20">
##FILTER=<ID=hp10,Description="Reference homopolymer length was longer than 10">
##FILTER=<ID=fr0,Description="Non-ref allele is not covered by at least one read on both strands">
##FILTER=<ID=wv,Description="Other indel in window had higher likelihood">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
Post edited by Geraldine_VdAuwera on
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