I was skimming through that study earlier to find out how they calculated their rate and their methods. Really cool they ended up confirming family history.
I don’t know if you noticed my hypothesis earlier about the same mutations occuring in different lineages (I guess that’s called parallel mutations?). So this caught my attention.
To estimate the potential sequencing error rate, we applied a phylogenetic approach. We checked whether we found all SNPs in the BigY captured region which are known to be phylogenetically located between haplogroups A0 and G (www.isogg.org) and thus should be present in our samples. The proportion of missed SNPs was the false negative rate. We also checked whether we see SNPs known to define other haplogroups, which are therefore not expected to be present in our haplogroup G samples. The proportion of these unexpected SNPs was considered as the false positive rate. We note that this approach overestimates the error rate, because it considers parallel mutations as errors and ignores potential inaccuracies in identifying the SNP ancestral states in ISOGG database. The (over)estimated rates were 0.008 for false negatives and 0.005 for false positives. (See details in S2 Table
That is quite the error rate compared to Lauritz Skov. Maybe the methods are different enough, but it makes me wonder about back mutations. So yes, I still want more father-son studies specifically.
Uh, what? 
Was that reaction the point? If so, point made. 
If not, please explain.
I wrote the above and then went back to look at Balanovsky because I was curious how they described filtering before I finished my post. I clicked on Supplementary Table 2 and then was looking at the number of false negative and false positive SNPs and then…I saw what they wrote behind the asterisks at the bottom. I thought my hypothesis about parallel mutations occuring often was a pretty good idea, but when I looked at the error rate listed there compared to what’s in the main text of the paper…I haven’t picked my jaw up off the floor yet.
Im sharing a screenshot but it’s probably tiny so you’ll have to go look for yourselves.
