All Questions
9 questions
7
votes
1
answer
120
views
How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're ...
- 73
2
votes
1
answer
65
views
Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing ...
- 123
3
votes
1
answer
93
views
Rigorous definition of the kinship coefficient and proof of a recursion thereof
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
- 486
3
votes
1
answer
9k
views
What are Codominant vs Dominant Genetic Markers?
When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions.
Foll and ...
- 68.3k
1
vote
1
answer
602
views
ExAC Browser: What does a "dubious variant annotation" mean? [closed]
I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC.
I couldn't find any further information neither at the ...
- 111
2
votes
1
answer
546
views
How to get the average number of pairwise differences among populations?
I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of ...
- 68.3k
1
vote
0
answers
40
views
How does one calculate Rx/a in population genetics?
The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?
- 11
1
vote
0
answers
19
views
Is there any data to explore the heterozygosity of the South African lion over the last 18 years?
Background:
I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point.
Question:
Where can I find ...
- 3,597
2
votes
0
answers
128
views
Efficient algorithm to calculate various population divergence statistics
Intro and description of the data
I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format
...
- 68.3k