I recently encountered the term "BAF" in a post on Biostars. I've looked up the definition, which is "B-Allele Frequency" (the extended definition is no more enlightening; one allele is A and the other is B). To me, that has no meaning other than being "Allele Frequency" with perhaps implicit assumptions about ploidy that are not generalizable, or maybe assumptions about the major/minor allele counts (from sequencing depth), or perhaps population frequencies, or maybe the reference allele. Can anyone explain where BAF is a useful term, or when one should use "BAF" instead of "AF"?
I've mostly seen BAF used in the context of SNP arrays, when there are two probes (an A probe and a B probe) covering a specific position. I think the A probe is generally the reference sequence (or was at the time the array was designed), so BAF and AF end up being the same, with the exception that SNP arrays are obviously limited in what they can detect.
I think this is a good explanation: https://www.ogt.com/resources/literature/768_cytosure_interpret_software_tips_and_tricks
Is principally used in CNV arrays.
"The B-Allele Frequency is a normalized measure of the allelic intensity ratio of two alleles (A and B), such that a BAF of 1 or 0 indicates the complete absence of one of the two alleles (e.g. AA or BB), and a BAF of 0.5 indicates the equal presence of both alleles (e.g. AB)."
It is a usefull measure when you are studying CNVs (LOHs or also SVs):
" detection of allelic imbalances such as those caused by duplications (e.g. AAB/BBA) or mosaic deletions in the sample. Such imbalances can be identified on a BAF plot by the presence of SNPs at frequencies between 0.5 and 0 or 1. For example, the theoretical BAF values of triploid regions (AAA, AAB, ABB or BBB) are 0, 0.33, 0.66 and 1 respectively."