Questions tagged [haplotypes]
Genetic code involving inherited DNA present as a single copy, which for eukaroyotes is the mitochondrion and in bacteria is the complete genome.
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How to plot a graph of Linkage disequilibrium with limited information
I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, ...
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1answer
17 views
How do I infer someone's haplotype of a gene from data on several of the gene's SNPs?
For a a few SNPs from given gene, I know there happen to be several haplotypes that most of the population has. But from a person's data on those SNPs, we have two alleles at each SNP, so it's not ...
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1answer
34 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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3answers
46 views
Genotyping technologies do not maintain phase?
Why exactly does genotyping not maintain phase? I guess I'm more confused on what's the difference between sequencing and genotyping, and as a result how phase is maintained in one, but not the other. ...
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1answer
195 views
Searching tool to calculate phase/switch error rate
I'm looking for a tool which, given a truth vcf file and a test vcf file, calculates the phase/switch error rate. I performed phasing of a vcf using WhatsHap and want to compare the outcome to some ...
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1answer
112 views
Highly heterozygous reads mapping
I have short (67bp) Hi-C reads from a highly heterozygous organism (~15% between-haplotype SNP divergence) and I have both reference haplotypes.
I wanted to try and compare different haplotyping ...
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457 views
How to format the Nexus file to create geographical maps with haplotypes in PopArt?
I'm trying to create a map in PopArt that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks:
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3answers
117 views
Sampling haplotypes
I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project.
I want to simulate different whole genomes i.e generate a new population by ...
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1answer
293 views
How to download SNP data from specific regions, population and positions?
I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems.
To do that, I've read a lot of papers and books in order to understand the main ...
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1answer
477 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.
5
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1answer
107 views
How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?
I have crossposted this question in maths StackExchange. The problem is dominantly mathematical (this question) but the application of the problem is mainly biological. Hoping that people in this ...
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403 views
How to indicate the END of a haplotype block in VCF?
In VCF I know how to indicate that two genotypes are in the same phase by using consecutive "0|1" and "1|0" genotype fields, for example. However, how do I deal with the case that the first two ...
