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
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Is SNPRelate the goto package for PCA of SNP data in R?
I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?
Many thanks,
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Nucleotide diversity obtained from Arlequin
I am calculating nucleotide diversity using Arlequin, from DNAsp6 Output. I've seen that the DNAsp6 output contain information about the haplotypes that I am analyzing. In base of the input data I ...
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29 views
How to know the number of SNP in my samples after running the population module in stacks
I am new to stacks for analyzing RAD-Seq data, I have run all the modules. I will like to know to get the total SNP from my sample after running the population module. Is there a command line to use ...
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35 views
PCA analysis and nucleotide diversity pi
I have 25 individuals' whole-genome sequence (collected from 5 different locations) and after doing a variant calling analysis, I found 2734 SNP+INDELS marker (SNPs + INDELS = 2734 ). Then I plot the ...
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40 views
RAD Seq Data Analysis without barcode
I received a ddRAD Seq data from my supervisor without barcodes and restriction enzymes. I asked him for both and he said I don't need it since the data has been cleaned by the company. Now, I am ...
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1answer
26 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, ...
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1answer
44 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 ...
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1answer
51 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, ...
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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 ...
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1answer
31 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 ...
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1answer
96 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 ...
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2answers
121 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 ...
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1answer
87 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 ...
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1answer
46 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 ...
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1answer
33 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 ...
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1answer
40 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 ...
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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 ...
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1answer
60 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.
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1answer
95 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
...
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20 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 ...
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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 ...
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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/...
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132 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 ...
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78 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 ...
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1answer
282 views
What is Allelic Imbalance
Can anyone help me explain what allelic imbalance is, hopefully shortly?
Surprisingly, we cannot find any introduction online.
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1answer
139 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 ...
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1answer
138 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 ...
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2answers
91 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 ...
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126 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 ...
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1answer
82 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.
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1answer
472 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.
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1answer
75 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 ...
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1answer
100 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 ...
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1answer
269 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 ...
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4answers
1k 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 ...
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1answer
197 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 ...
