Genetic Variants and ChIP-seq data: When we are working with patient samples for ChIP-seq, we align them all to one generic reference genome. Will the alignment tolerate and SNPs in the individual patient line?

Yes. The alignment algorithms will treat individual SNPs as mismatches compared to the reference genome and should be able to easily handle them. Usually these algorithms are made to tolerate several mismatches per read. -answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.