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combine snp and indel vcf
is there any way to combine a snp vcf and indel vcf (generated with the UnifiedGenotyper) later? in the way that there is only one row per locus?
regardless how I combine (I tried mainly CombineVariants), if there is something different called in the two vcf files in one locus, there are two rows in the combined one; I would like this called/written as alternatives for one locus