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VariantAnnotator Annotation Error

MaxideSousaMaxideSousa ArgentinaMember

I'm trying to annotate using VariantAnnotator, when I run:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R ucsc.hg19.fasta --variant LK8851-Clean.vcf --resource LK8851-Clean-snpEff.vcf -L LK8851-Clean.vcf -o LK8851-Clean-VA.vcf

I get the following error:

Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data

One of the variant lines:

1 14907 rs79585140 A G 661.53 MQFilter40 . .

I downloaded the vcf from and had to add the "." in the INFO and FORMAT columns because I was getting the error:

Line 128: there aren't enough columns for line 1 14930 rs75454623 AG 1103.37 MQFilter40 . (we expected 9 tokens, and saw 8 )

I'm new to this, I really searched a lot, but couldn't find anything useful, probably a very stupid error, but I would really appreciate your help.

Thank you for your time,

Best Answers


  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Maxi,

    How did you produce the input VCF file LK8851-Clean.vcf? What exactly are you trying to achieve by running Variant Annotator?


  • MaxideSousaMaxideSousa ArgentinaMember
    edited July 2015

    Hi Sheila,

    I downloaded the vcf from a pacients data bank from the Personal Genome Project, I erased the annotated info, so as to try and compare how different annotation programs work and what kind of info they add. Now I`m trying to get all the info VA can provide, understand it and decide if I will be using it on my pipeline for human genomic analysis for my PhD.


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