Questions tagged [population-genetics]

Disapline mostly concerned with allele frequencies to define the intraspecific (intra-species) population structure, but can be applied to phenotypic outcome, e.g. Medel's pea plants

Filter by
Sorted by
Tagged with
0
votes
1answer
16 views

Loss of predictive power of polygenic risk score when dataset contains missing variants

I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
1
vote
1answer
36 views

Apply trained PRS on another dataset

I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set. Once I compute the PRS I get a ...
2
votes
1answer
44 views

Populations genetics and dynamics of bacteria on a Graph

Disclaimer: I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense. My purpose: I would like to simulate genetic evolution of bacterial populations, ...
0
votes
2answers
37 views

Tracing and quantifying inheritance over many generations

Apologies if this is the wrong location for this question, and please feel free to point me in the right direction with appropriate Anglo-Saxon embellishments... I'm after some ball-park numbers for ...
0
votes
1answer
20 views

STRUCTURE interprets pop ID as locus

I'm using structure for the first time and I fail to execute a "job". For some reason, structure interprets the ...
1
vote
1answer
31 views

Time for running ADMIXTURE analysis

I am trying to run the ADMIXTURE software for the first time to analyse the structure of an in-house dataset of samples comparing to 1000 genomes project ancestral populations. I am trying to ...
5
votes
2answers
116 views

Does the kinship and inbreeding coefficients depend on population frequency of an allele?

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 ...
1
vote
1answer
60 views

Power calculation for GWAS/EWAS

I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease. I wonder, does anyone has came across ...
2
votes
1answer
42 views

List of global ethnicities

Looking at the 1000 genomes project I see the following list of population groups and super-groups: https://www.internationalgenome.org/category/population/ However, is there something like a ...
1
vote
1answer
27 views

Generate an approapite output from DNaSP6 to Arlequin program

I am performing a haplotype and nucleotide diversity of my Sanger sequences (from Watermelon mosaic virus coat protein region) by Arlequin program with the aim to see the probability that two randomly ...
1
vote
1answer
39 views

How to compute Shanon entropy

I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
1
vote
0answers
35 views

Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
1
vote
1answer
36 views

What software can I use to develop a population haplotype network?

I looking for software to conduct a haplotype network using cytochrome oxidase (CO1) mitochondrial sequence data to study population structure in Anopheles mosquitoes.
2
votes
1answer
75 views

How to interpret Mendelian randomization results?

I did Mendelian randomization using this software: https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf ...
1
vote
0answers
19 views

the positions computed by ms

I am doing simulations using a program 'ms': https://snoweye.github.io/phyclust/document/msdoc.pdf If you look at page 3 of this pdf, it explains the output produced by ms. The line which starts ...
1
vote
1answer
45 views

Confusion related to effective population size

I am making a demographic model for African American population in which I say 80% of ancestry comes from African population and 20% comes from European population. I am using the time/population time ...
2
votes
1answer
61 views

Demographic model for admixed African Americans

I am fairly new to genomics and population genetics. And I am reading this article 'Demographic history and rare allele sharing among human populations': https://www.ncbi.nlm.nih.gov/pmc/articles/...
1
vote
0answers
114 views

Geneland R + Fortran error?

I am helping an undergrad with their project and their thesis advisor has requested they use GENELAND for their analysis. I haven't worked on this sort of analysis, so all I have done is install it in ...
5
votes
0answers
71 views

making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)?

Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is ...
6
votes
1answer
250 views

What is Allelic Imbalance

Can anyone help me explain what allelic imbalance is, hopefully shortly? Surprisingly, we cannot find any introduction online.
6
votes
1answer
125 views

What is the minimum number of individuals per group required for ADMIXTURE analysis?

What is the minimum number of individuals required per group (population/species) for an ADMIXTURE analysis to be appropriate? Is there a way to determine this number mathematically based on the ...
5
votes
1answer
120 views

Simulating DNA sequence evolution in R

I hope someone can lend their thoughts on the below code to generate DNA sequences under the Kimura-2-Parameter model of DNA substitution. The issue is that each time the code is run and the ...
5
votes
2answers
84 views

How do population genetics people define a population?

How do population genetics people define a population? Do they define it as a layman will do? say Africans, Americans, or so? Or is there a more scientific way of doing so? For example, I think ...
2
votes
0answers
106 views

Reproducing population structure from 1000 Genomes Data

I recently tried to reproduce population structure with 1000 Genomes Project data (Phase 3, 2504 people). According to supplementary material, To reduce the dataset, we used VCFtools to only keep ...
4
votes
1answer
77 views

Statistical approach to compare the SNP genotyping data among set of individuals

So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. ...
2
votes
1answer
417 views

Program to make a haplotype network for a specific gene

Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. Example: I just feel like there's got to be a better, more time effective way to do this.
1
vote
1answer
73 views

How do programs like STRUCTURE determine populations from alignments?

If I were to run BAM/SAM files through a program like STRUCTURE, or ADMIXTURE described here how would they determine which individuals belong to what groups? What part of the files would these ...
1
vote
1answer
99 views

population admixture

I am new to Admixture and I would like to use fastNGSadmix to look for admixture in one individual (modern). Admixture is supposed to look for proportions of ancestral populations in a sample (either ...
1
vote
1answer
225 views

Where can I find a list of SNP rs IDs that belong to the X chromosome?

Where can I find a list of SNP rs IDs that belong to the X chromosome? I'm trying to exclude the SNPs on X-chromosome in a data set, but I don't know where these SNPs come from. I tried to use ...
4
votes
4answers
995 views

Convert rs ID of one hg build to rs IDs of another build

I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping ...
2
votes
1answer
176 views

How is a principal component analysis for population structure made from a bam or other alignment file?

I'm curious how a PCA for population structure is built from an alignment/BAM or SAM file. How do programs like angsd and ngsCovar actually build a PCA? What exactly makes things come out as different ...