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Questions tagged [haplotypes]

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38 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. ...
5
votes
1answer
85 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 ...
8
votes
1answer
74 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 ...
1
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0answers
76 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: ...
5
votes
3answers
95 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 ...
1
vote
1answer
96 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 ...
2
votes
1answer
281 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
votes
1answer
98 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 ...
5
votes
3answers
255 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 ...