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
vcf1
21 11098723 . T C
21 11098724 . G A
vcf2
21 11098723 exm1562347 A G
how can i fix this error?