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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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8 votes
1 answer
143 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 ...
cmdoret's user avatar
  • 595
5 votes
3 answers
526 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 ...
Dan's user avatar
  • 612
5 votes
3 answers
127 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 ...
Kozolovska's user avatar
5 votes
1 answer
405 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 ...
Wouter De Coster's user avatar
5 votes
1 answer
118 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 ...
everestial's user avatar
3 votes
1 answer
80 views

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' ...
Dan Bolser's user avatar
2 votes
1 answer
78 views

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 ...
rimo's user avatar
  • 1,003
2 votes
1 answer
649 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. I would like to know how to generate the graph structure (i.e. the links between vertices), ...
Ryan Fahy's user avatar
1 vote
3 answers
51 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. ...
Jonathan's user avatar
  • 341
1 vote
1 answer
459 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 ...
William Tenorio's user avatar
1 vote
1 answer
65 views

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 ...
Dan Bolser's user avatar
1 vote
1 answer
164 views

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 ...
Adrián P.L.'s user avatar
1 vote
0 answers
53 views

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/...
Mahmood Hasan's user avatar
1 vote
0 answers
58 views

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 ...
Roa.tar's user avatar
  • 11
1 vote
0 answers
25 views

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 ...
Anik Dutta's user avatar
1 vote
1 answer
72 views

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 ...
Jason H's user avatar
  • 13
1 vote
0 answers
1k 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: ...
LinuxBlanket's user avatar
0 votes
1 answer
30 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 ...
user1799035's user avatar
0 votes
0 answers
186 views

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, ...
Ugur Toprak's user avatar