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CombineVariants-- inconsistent references error

Hi I have 2 vcf files
vcf1 from WGS data
vcf2 from genotype data
I am trying to merge these two files using combinevariants
java -jar $GenomeAnalysisTK_jar -T CombineVariants -R $REF --variant $vcf1 --variant $vcf2 -o $outputfile

I am getting this error

MESSAGE: The provided variant file(s) have inconsistent references for the same position(s) at 21:11098723, T* vs. A*

ERROR ------------------------------------------------------------------------------------------

when i grep these position in

21 11098723 . T C

21 11098724 . G A


21 11098723 exm1562347 A G

how can i fix this error?

Best Answer


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