According to my experience the f3-analysis (and dstat) generates error due to differences in SNP numbers between individuals. Because the SNP number can vary as to the sample source, I removed all "bad" SNPs from the study data and added Finnish samples to make it equal to other sample groups. Actually the average SNP amount in individual tests didn't change much from the original situation, with exception of samples gathered from the 1000genomes project. After this operation the SNP number in each test between ancient and modern samples was almost constant.
Average SNP numbers per ancient sample, the difference inside one test group a few hundreds in maximum
WEZ15 56606
WEZ16 5453
WEZ24 13749
WEZ35-2 28766
WEZ39 9343
WEZ40 21711
WEZ48 6392
WEZ51 15313
WEZ53 14758
WEZ54 29468
WEZ56 28034
WEZ57 34161
WEZ58 21152
WEZ59 28256
WEZ61 34657
WEZ63 11920
WEZ64-1 26150
WEZ71 15698
WEZ74 9891
WEZ77 15721
WEZ83 14999
Result of f3-tests using Mbuti as an outgroup:
All data with exception of Finnish samples (1000genomes) are from the study
Addressing Challenges of Ancient DNASequence Data Obtained with NextGeneration Methods
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