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Old 10-06-2011, 07:04 AM   #1
tomato2
Junior Member
 
Location: chapel hill

Join Date: Sep 2011
Posts: 2
Default GATK VariantRecalibrator

Hi,

I tried GATK's VariantRecalibrator on a raw.vcf obtained from UnifiedGenotyper.

Although my input vcf file has a CHROM header line (starting with one #), GATK gives me an error saying " ERROR MESSAGE: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file".

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.2-21-g6804ab6):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
##### ERROR ------------------------------------------------------------------------------------------

Can anyone give me some advice to deal with this error?

Thanks a lot.
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Old 05-06-2012, 03:28 AM   #2
soeren perrey
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Location: muenster

Join Date: Oct 2011
Posts: 2
Default malformed header

your header needs the appropriate number of columns,e.g.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chrM 195 . C T 118.58 LowCoverage AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=254.00;MQ0=0; QD=29.64;SB=-36.53; QSLOD=13.0122;culprit=MQ GT:ADP:GQ:PL 1/1:0,4:4:12.04:151,12,0Sample_01

cheers,

soeren
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