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Merge VCF files after Beagle : bad option for CombiVariants
I don't understand error message from CombiVariants. I uses a command line from http://gatkforums.broadinstitute.org/discussion/43/interface-with-beagle-software#Merging_VCFs_broken_up_by_chromosome_into_a_single_genome-wide_file.
In documentation, you talk about this option : - variantMergeOptions UNION. But in your example, you give this option -type UNION.
But none of these options exists. I find only this option variantMergeOptions.
what is the good option and the value of this option to merge all vcf files from all chromosomes phased by beagle?