How many have new 'Multiple Nucleotide Polymorphisms' in their results?

[Cofgene]

The Big Y (and FGC Elite) tests are discovering a handful of 2 bit MNPs (Multiple Nucleotide Polymorphisms). This is where two side-by-side bases are changed. Depending on who is doing the calling the you may see a single SNP call or two SNP calls. What we need to understand is their rate of occurrence. Depending on the rate of occurrence compared to SNPs in Big-Y results some of the SNP counting age determination methods may need a filter for MNPs.

Note that the existence of MNP's will require an adjustment in the ISOGG Y-tree quality criteria to support them.

[JamesKane]

I'm currently running a very large ReadBackPhasing batch job on 341 BAMs to identify the MNPs. The set has one at chrY:6762207..6762208 AC->CG that Nigel McCarthy identified earlier for sure. A naive search turns up about 400 other candidates, but they all need to be verified. The run time will likely take over a week.