@eupator
i ran the f3 comparisons:
with the HO dataset, sorted from the most similar population to least:
with the 1240k dataset, to check if it's consistent when more SNPs are used:
code used to run it:
i ran the f3 comparisons:
with the HO dataset, sorted from the most similar population to least:
Code:
pop1 pop2 pop3 est se z p
Mbuti Greece_BA_Mycenaean Sardinian 0.0692 0.000538 129 0
Mbuti Greece_BA_Mycenaean Italian_North 0.0686 0.000534 129 0
Mbuti Greece_BA_Mycenaean Albanian 0.0683 0.000548 125 0
Mbuti Greece_BA_Mycenaean Greek 0.0682 0.00053 129 0
Mbuti Greece_BA_Mycenaean Greek.WGA 0.0681 0.000528 129 0
Mbuti Greece_BA_Mycenaean Bulgarian 0.068 0.000535 127 0
Mbuti Greece_BA_Mycenaean Cretan.DG 0.0677 0.000596 114 0
Mbuti Greece_BA_Mycenaean Greek_outlier.WGA 0.0677 0.000579 117 0
Mbuti Greece_BA_Mycenaean Sicilian 0.0675 0.00054 125 0
Mbuti Greece_BA_Mycenaean Armenian 0.0674 0.000527 128 0
Mbuti Greece_BA_Mycenaean Italian_South 0.0674 0.000536 126 0
Mbuti Greece_BA_Mycenaean Turkish 0.0667 0.000519 129 0
Code:
Mbuti Greece_Minoan_Lassithi Sardinian 0.0693 0.000489 142 0
Mbuti Greece_Minoan_Lassithi Italian_North 0.0684 0.000487 140 0
Mbuti Greece_Minoan_Lassithi Albanian 0.0682 0.000503 135 0
Mbuti Greece_Minoan_Lassithi Greek 0.068 0.000486 140 0
Mbuti Greece_Minoan_Lassithi Bulgarian 0.0678 0.000487 139 0
Mbuti Greece_Minoan_Lassithi Greek.WGA 0.0678 0.000481 141 0
Mbuti Greece_Minoan_Lassithi Cretan.DG 0.0677 0.00055 123 0
Mbuti Greece_Minoan_Lassithi Italian_South 0.0677 0.000495 137 0
Mbuti Greece_Minoan_Lassithi Greek_outlier.WGA 0.0675 0.000532 127 0
Mbuti Greece_Minoan_Lassithi Sicilian 0.0673 0.000497 136 0
Mbuti Greece_Minoan_Lassithi Armenian 0.0672 0.000485 139 0
Mbuti Greece_Minoan_Lassithi Turkish 0.0665 0.000474 140 0
with the 1240k dataset, to check if it's consistent when more SNPs are used:
Code:
Mbuti.SDG Greece_Minoan_Lassithi Sardinian.SDG 0.0739 0.000528 140 0
Mbuti.SDG Greece_Minoan_Lassithi Albanian.DG 0.0731 0.000608 120 0
Mbuti.SDG Greece_Minoan_Lassithi Greek.DG 0.073 0.000554 132 0
Mbuti.SDG Greece_Minoan_Lassithi Italian_North.SDG 0.073 0.000524 139 0
Mbuti.SDG Greece_Minoan_Lassithi Tuscan_1.DG 0.0728 0.000572 127 0
Mbuti.SDG Greece_Minoan_Lassithi Bulgarian.DG 0.0725 0.000543 133 0
Mbuti.SDG Greece_Minoan_Lassithi Cretan.DG 0.0724 0.000575 126 0
Mbuti.SDG Greece_Minoan_Lassithi Armenian.DG 0.0715 0.000555 129 0
Mbuti.SDG Greece_Minoan_Lassithi Turkish.DG 0.071 0.000582 122 0
code used to run it:
Code:
library(admixtools)
prefix = 'v50.0_HO_public'
my_f2_dir = 'myf2'
extract_f2(pops=c('Mbuti','Greece_Minoan_Lassithi','Greek','Cretan.DG','Greek.WGA','Greek_outlier.WGA','Albanian','Bulgarian','Italian_South','Italian_South','Sicilian','Sardinian','Italian_North','Armenian','Turkish'),maxmem=4000,prefix,my_f2_dir, fst=FALSE, afprod=FALSE,maxmiss = 1)
f2_blocks = f2_from_precomp(my_f2_dir)
pop1 = 'Mbuti'
pop2= 'Greece_Minoan_Lassithi'
pop3 = c('Greek','Cretan.DG','Greek.WGA','Greek_outlier.WGA','Albanian','Bulgarian','Italian_South','Italian_South','Sicilian','Sardinian','Italian_North','Armenian','Turkish')
qp3pop(f2_blocks, pop1, pop2, pop3)