The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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.