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CombineVariants fail when combining vcf from genotypeGVCFs genotyped using -allSites flag
When I attempt to run the tools CombineVariant with two vcf files generated from GenotypeGVCFs using the flag -allSites I get an error saying that I should not use combineVariants in a gvcf file. But my files are not gvcf.
ERROR MESSAGE: CombineVariants should not be used to merge gVCFs produced by the HaplotypeCaller; use CombineGVCFs instead
java -jar GenomeAnalysisTK.jar
gatk version v3.7-0
If I run it in the vcfs from GenotypeGVCFs not using the flag -allSites, I don't get this error and it runs fine.