It used to be possible to annotate a VCF files using multiple VCF track files. Basically the --comp command could be used multiple times. Now only the last track gets annotated. That means, if I use "-T VariantAnnotator --comp:TR1 tr1.vcf --comp:TR2 tr2.vcf, only the TR2 flag is used for annotation, and the TR1 flag is not. This is inconsistent and must be a recent regression.
It works fine with GenomeAnalysisTK-2.5-2 but it doesn't work anymore with GenomeAnalysisTK-2.6-2.