An important message from Nick Patterson:
Dear Eurogenes bloggers,
Many of you use ADMIXTOOLS and you might like to know that there is a new release on github [LINK] with some important enhancements.
From the README
*** NEW ***
1)
Version 7.0 has numerous upgrades.
a) Two new executables --qpfstats qpfmv allow precomputation of f-statistic basis. This can greatly reduce computation costs.
b) qpAdm, qpWave, qpGraph support qpfstats output as input.
*** This is a much improved way of running with allsnps: YES. ***
c) A new experimental feature of qpGraph (halfscore: YES) allows comparison of 2 phylogenies + a (weak) goodness of fit score. Be careful if running with a large number of populations and consider reducing block size say blgsize: .005
2)
Note that several of the new ideas implemented in version 7.0 were developed collaboratively with Robert Maier, who has implemented them along with the great majority of other ADMIXTOOLS functionality in R: See https://github.com/uqrmaie1/admixtools
Executables run fast, and it has features not available in this C version, such as interactive exploration of graph phylogenies.
A manuscript describing the algorithmic ideas and providing documentation of the methods is in preparation.
qpfstats is the most important new executable. This estimates f-statistics and covariance on a basis.
a) This can be passed into other programs of the package without having to reaccess the genotype files, greatly speeding the computations.
b) In allsnps: YES mode a new computation is carried out (explained in qpfs.pdf) that is much more logical when there is a lot of missing data. Sometimes standard errors are greatly reduced.
qpfstats can be used with up to 30 populations. Much beyond that the output files become large.
As usual there may be bugs...
Nick Patterson 6/27/2020
Update 29/06/2020: As pointed out above, qpfstats is the most important new executable. Indeed, Nick Patterson now recommendeds that qpAdm analyses run with the
allsnps: YES flag should be based on qpfstats output.
Several of my recent blog posts featured qpAdm models run with the
allsnps: YES flag, but they were based on genotype data because obviously I didn't know anything about qpfstats at the time.
So I went back and ran some of these models again, just to make sure that they were still relevant. Below are three examples which you can compare to the original analyses
here,
here and
here, respectively.
TUR_Arslantepe_LC_Maykop
RUS_Maykop_Novosvobodnaya 0.281±0.042
TUR_Arslantepe_LC 0.719±0.042
chisq 10.923
tail prob 0.449752
Full output
TUR_Barcin_C
RUS_Vonyuchka_En 0.137±0.031
TUR_Buyukkaya_EC 0.863±0.031
chisq 15.074
tail prob 0.0889099
Full output
UKR_N_admixed
RUS_Progress_En 0.083±0.020
UKR_N 0.917±0.020
chisq 6.825
tail prob 0.65538
Full output
As far as I can tell, they're very similar to the original runs, which is a relief, because it means that the conclusions in my blog posts still make sense.
