Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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
vcf1

21 11098723 . T C

21 11098724 . G A

vcf2

21 11098723 exm1562347 A G

how can i fix this error?

Best Answer

Answers

Sign In or Register to comment.