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malformed header: No required CHROM header line (starting with one #)

PandapiggiePandapiggie JapanMember
edited November 2015 in Ask the GATK team

Sorry if this has been answered previously but I couldnt find any troubleshoot for this. I was using vcf-annotate to annotate my vcf files generated using GATK Haplotype caller. I tried to then use the GATK Select variants to separate the SNP and INDELS and I got this error msg

"Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file"

This is the head of the vcf file.

##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=NC_003198.1,length=4809037>
##reference=file:///home/jason/redone/ct18ncbi.fasta
##INFO=<ID=ANN,Number=1,Type=Integer,Decription="My custom annotation-r">
##source_20151109.1=vcf-annotate(r840) -a ct18.annotate.gz -d key=INFO,ID=ANN,Number=1,Type=Integer,Decription=My custom annotation-r -c CHROM,FROM,TO,INFO/ANN
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sorted_trial2
NC_003198.1 13276   .   C   T   4694    .   ANN=dnaK    GT:AD:DP:GQ:PL  1:0,121:121:99:4724,0
NC_003198.1 22623   .   T   C   4340    .   ANN=STY0019 GT:AD:DP:GQ:PL  1:0,122:122:99:4370,0

I have compared this to previous file (before annotation) and it is same, except the addition of the

##INFO=<ID=ANN,Number=1,Type=Integer,Decription="My custom annotation-r">
##source_20151109.1=vcf-annotate(r840) -a ct18.annotate.gz -d key=INFO,ID=ANN,Number=1,Type=Integer,Decription=My custom annotation-r -c CHROM,FROM,TO,INFO/ANN

Hope you can help me understand the error location.

Thank you.

Jason

Best Answers

Answers

  • PandapiggiePandapiggie JapanMember

    I used the vcf-annotate tools from vcftools.

    I removed the line in excel and the error still persist. How should I go about removing that line?

    Thanks.

  • PandapiggiePandapiggie JapanMember

    Thank you Geraldine. Your comment help me solve the issue

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @Pandapiggie Great that your problem was solved :) Excel spawned in hell unless doing your budget for next year. If I remember correctly you are not allowed to have spaces without double quotes. Furthermore page 5 of the VCFv4.3 file format specification reads:

    Meta-information lines can be in any order with the exception of ‘fileformat‘ which must come first.
    
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