Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.