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VariantFiltration, masking variants

When using one vcf to mask variants in another, does VariantFiltration take into account the nucleotide change at a given position? I was attempting to use 'Control' samples to mask changes in 'Experimental' samples and noticed that, as an example the 'Control' vcf would have a C > T at a genomic position, the 'Experimental' samples would have a C > G at that same position, but would still be masked. For our purposes, these are not equivalent.

Is this working as intended? Is there perhaps a better way to accomplish the type of masking/filtering I want? Thank you.

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