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

You just searched for X[Chromosome], you didn't specify a species. Presumably, your dataset comes from a specific species, so you should limit your search to that ...
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  • 8,121
5 votes
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What is Allelic Imbalance

It might be used differently in different contexts, but generally speaking, in my world - allelic imbalance is when there's a difference in the level of gene expression from different alleles, usually ...
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  • 184
5 votes

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

You can assume that the overwhelming majority of rsIDs are the same between GRCh37 and GRCh38 (they're semi-stable IDs). There are, however, a number of rsIDs that are present only in GRCh37, which ...
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  • 19.2k
4 votes
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How is a principal component analysis for population structure made from a bam or other alignment file?

In general, the process works as such: Variants are found at a number of loci in each sample (missing loci are often imputed). Each sample is scored at each locus, often according to the number of ...
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  • 19.2k
3 votes
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Populations genetics and dynamics of bacteria on a Graph

I assume you are simulating a null distribution. Are you investigation recombination?? My main advice is to use population genetic terminology rather than geomometry to describe your simulation (e.g. ...
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  • 7,349
3 votes

How do population genetics people define a population?

A population is defined as a group of people (or organisms of the same species) living together in a geographical region. However, for human genetic studies, it is wise to use ethnicity as well (so ...
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  • 3,541
3 votes
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Statistical approach to compare the SNP genotyping data among set of individuals

PCA sounds like a good start to see a rough population structure among your 96 individuals, this step is half a sane thing to do, but also it can give you a hint how many distinct populations there ...
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  • 5,287
2 votes
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Convert rs ID of one hg build to rs IDs of another build

Did you try the liftOver tool of UCSC? You'll need a BED file with your SNPs coordinates for this. You can also do this in R with ...
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  • 3,541
2 votes
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How do programs like STRUCTURE determine populations from alignments?

structure works with SNP/genotype information, so won't work directly off BAM/SAM files. You would need to convert to VCF (e.g. using mpileup/vcftools), then process using something like PLINK to ...
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2 votes

population admixture

Disclaimer, I am not an expert on admixture, answer is provided without any warranty. It depends what you want to figure out. Why do you want to categorize the ancestry of the individual? If you ...
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  • 5,287
2 votes

How to compute Shanon entropy

I think there needs to be clarification of the question. Shannon entropy is not the same thing as the Shannon-Wiener diversity index (H), commonly referred to as the Shannon index. The reason I ...
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  • 7,349
2 votes
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Does the kinship and inbreeding coefficients depend on population frequency of an allele?

The definition as set by Kenneth Lange's book is indeed quite vague and thus unrigorous. It is a probability not conditioned on observing any particular allele at a locus thus not on the population ...
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  • 179
2 votes
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RAD Seq Data Analysis without barcode

Wow Biobash, that's kinda harsh. It is cool that sometimes you unexpectedly learned something new. What Michael mentioned is pretty interested, no one has ever mentioned that or I have never heard ...
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2 votes
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How do population genetics people define a population?

It really depends on the study and the ethnicity. Mostly they use self-defined ethnicity and often they will require that three or four grandparents are of that ethnicity. Here's some detailed info on ...
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2 votes

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

Ultimately, I achieved this using the R package strataG. The steps taken (in R) are shown below. ...
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2 votes
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LD Score Regression Derivation hard to follow

Not entirely clear on what you're asking but the beta estimates in LDSC come from GWAS summary statistics. As I understand it, they aren't "derived" so much as just set equivalent to what ...
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1 vote

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

First focus on calling SNPs accurately. See the BWA, SAMtools, BCFtools pipeline (as described here) or GATK4 (as described here). Once you have the [BV]CFs, then just code up the analysis to see ...
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1 vote

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

Not in the way you suggest: a sequence of letters with the property of being immutable by any type of permutation on its constituent bases. I would be interested if anything of the likes exists in ...
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  • 353
1 vote

What is the tP statistic from ANGSD?

While I can't explain it to you directly, you might check out the section on theta estimators in Korneliussen et al. (2013) which is cited on the above ANGSD wiki page. The equation for this estimator ...
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1 vote

How to know the number of SNP in my samples after running the population module in stacks

Update Based on the newly provided command (which has --vcf), there should be a VCF file with suffix .vcf in the output ...
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1 vote

STRUCTURE interprets pop ID as locus

Hmmmm .... you don't actually need pop ID to work for Structure, providing their are no logical errors (you get a wrong answer). The bit that must work is the a priori number of populations in the ...
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  • 7,349
1 vote

Time for running ADMIXTURE analysis

Apparently there is a bug in ADMIXTURE that prevents for converging when using at the same time the haploid mode and multithreading (flags --haploid and -j respectively). The problem is solved by ...
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  • 21
1 vote

Power calculation for GWAS/EWAS

Interesting question I would recommend the effective population size $N_{e}$, and error bars around this. Ne can be calculated via $F_{st}$ and is perhaps the most important parameter to determine ...
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  • 7,349
1 vote

List of global ethnicities

It's not clear exactly what your goal is. It might help to have an idea of how you are trying to use this data; and it's probably not a bioinformatics question, as ethnicities are social/political ...
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1 vote
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Generate an appropriate output from DNaSP6 to Arlequin program

Yes, your question makes alot of sense and its a good question because hits at the heart of differences between population genetic analysis and phylogenetic analysis. However, when you speak about ...
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  • 7,349
1 vote

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

The software you are looking for is Network 5.0.0.3 Phylogenetic Network Software . Network © Copyright Fluxus Technology Ltd 1999–2018. Retrieved from https://www.fluxus-engineering.com/sharenet.htm ...
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  • 7,349
1 vote
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Demographic model for admixed African Americans

Just to further my answer, the problem with molecular dating within a species (I don't do humans [excepting immunology], but it's the same theory), is it requires an assumption of clonality (...
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  • 7,349
1 vote

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

The following paper provides an in-depth exploration of factors affecting power of admixture analyses under a number of different models. Although the authors state they "provide the open-source R ...
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  • 323
1 vote
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Simulating DNA sequence evolution in R

What are you expecting these lines to do? ...
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1 vote

Program to make a haplotype network for a specific gene

This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found here. The problem with manaul haplotype maps is the area of ...
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