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
2 votes
0 answers
21 views

What is the meaning of "Filtering allele frequency" in the gnomAD database?

Recent gnomAD versions include a "filtering allele frequency" which tells you when a variant can be safely adjudged not to be disease-causing. Unfortunately, I'm having trouble making sense ...
user avatar
  • 21
1 vote
0 answers
26 views

Convert Arlequin ("DNA" markers) to Genepop (PGDspider or otherwise)

I have Arlequin output files (*.arp) from fastSimcoal2 that I'm trying to convert to genepop files (to read into adegenet). The Arlequin files are using the "DNA" marker (50 bp long), and ...
user avatar
4 votes
1 answer
100 views

LD Score Regression Derivation hard to follow

I am trying to understand the derivations from Sullivan et al. (2015) in the Supplementary Material. There, it is mentioned in the first page that the least squares estimate of the j-th SNP effect, ...
user avatar
0 votes
1 answer
34 views

Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?

I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is... I have a VCF/PLINK format file of ~8,000 individuals ...
user avatar
0 votes
1 answer
26 views

What to use to determine SNPs in a population? How to find significant SNP variation between generations?

I have a population in the hundreds and did an Illumina pool-seq (ended up with ~100bp reads for the whole population). I have the reference genome for the species and now need to align all the ...
user avatar
0 votes
0 answers
34 views

Linking UK biobank patient IDs with their corresponding genetic data

I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs. I am trying to test with chromosome 5 as I have both bgen ...
user avatar
0 votes
1 answer
56 views

Is there any genetic sequence, such that, for all the kinds of mutation, it still has a 100% probability to be passed on?

This question is more on the theoretical-encoding side. Given the known kinds of genetic mutation, transposition, deletion, and such, what can be said about genes that would be left untouched by the ...
user avatar
1 vote
2 answers
31 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++ We used ANGSD to calculate ...
user avatar
  • 85
0 votes
0 answers
26 views

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,
user avatar
0 votes
1 answer
72 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 ...
user avatar
  • 19
2 votes
1 answer
49 views

Build tree to calculate beta diversity

I am trying to calculate beta diversity* using the UniFrac distance on my data, each sample having OTUs values. To calculate it, I saw it required building a tree with percentages that represented the ...
user avatar
  • 21
1 vote
0 answers
63 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 plotted ...
user avatar
  • 21
1 vote
2 answers
43 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 ...
user avatar
  • 19
0 votes
1 answer
38 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, ...
user avatar
1 vote
1 answer
45 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 ...
user avatar
  • 113
2 votes
1 answer
53 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, ...
user avatar
  • 123
0 votes
2 answers
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 ...
user avatar
  • 103
0 votes
1 answer
54 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 ...
user avatar
  • 123
1 vote
1 answer
258 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 ...
user avatar
  • 21
5 votes
2 answers
128 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 ...
user avatar
  • 179
1 vote
1 answer
128 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 ...
user avatar
2 votes
1 answer
60 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 ...
user avatar
1 vote
1 answer
66 views

Generate an appropriate output from DNaSP6 to Arlequin program

I am performing a haplotype and nucleotide diversity analysis of my Sanger sequences (from Watermelon mosaic virus coat protein region) using the Arlequin program. My aim is to see the probability ...
user avatar
1 vote
1 answer
53 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 ...
user avatar
1 vote
0 answers
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 ...
user avatar
1 vote
1 answer
85 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.
user avatar
2 votes
1 answer
121 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 ...
user avatar
1 vote
0 answers
21 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 ...
user avatar
  • 23
1 vote
1 answer
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 ...
user avatar
  • 23
2 votes
1 answer
62 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/...
user avatar
1 vote
0 answers
145 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 ...
user avatar
6 votes
0 answers
90 views

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

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 ...
user avatar
  • 61
6 votes
1 answer
296 views

What is Allelic Imbalance

Can anyone help me explain what allelic imbalance is, hopefully shortly? Surprisingly, we cannot find any introduction online.
user avatar
6 votes
1 answer
159 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 ...
user avatar
5 votes
1 answer
168 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 ...
user avatar
5 votes
2 answers
114 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 ...
user avatar
2 votes
0 answers
152 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 ...
user avatar
4 votes
1 answer
88 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. ...
user avatar
2 votes
1 answer
545 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. I would like to know how to generate the graph structure (i.e. the links between vertices), ...
user avatar
1 vote
1 answer
78 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 ...
user avatar
  • 87
1 vote
1 answer
109 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 ...
user avatar
  • 11
1 vote
1 answer
299 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 ...
user avatar
6 votes
4 answers
2k 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 ...
user avatar
  • 221
2 votes
1 answer
247 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 ...
user avatar
  • 87