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Questions tagged [population-genetics]

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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
38 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
56 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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72 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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0answers
39 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
54 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
93 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
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1answer
75 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
79 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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0answers
63 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
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1answer
67 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
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1answer
284 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
65 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
93 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
172 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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3answers
564 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
141 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 ...