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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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 ...
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What is the best way to process yeast genomes?
I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis.
I have a reference genome (S288C) to use for ...
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Weird data in VCF file
I am using GATK HaploTypeCaller for SNP calling. I have 300 samples. As far as I understand that if a sample is missing a SNP it should be denoted by ./., however, I am getting a lot of values like 0/...
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Imputing small region of the genome
If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' ...
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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), ...
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How to calculate switch errors on plink formatted phased genotype data?
everyone!
I'm working with haplotype inference algorithms in pedigree genotype data, and I would like to know if there is a tool or script to calculate switch errors on phased pedigree data (Plink ...
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Why does gene count increase drastically after scaffolding with Hi-C data?
I have a conceptual question.
I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
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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 ...
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Using a phased reference assembly to phase sample genotypes
I've been trying without success to phase the variants of about 30 samples in a 5Mb non-recombining region. I have a phased genome assembly of the region but so far I have not been successful in using ...
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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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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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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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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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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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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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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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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 ...
CommunityBot
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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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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 ...
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