Haplotype Reconstruction using PHASE · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Haplotype Reconstruction using PHASE

I am new to this field so my question is quiet naïve and stupid. For my data set, it look likes one snp of my gene of interest is under selection. I want to apply the ihs/ehh but before applying it, I have to reconstruct the haplotype. As I am interested in only one snp how should I select snps for haplotype reconstruction and how many snps should be selected? I am using PHASE for haplotype reconstruction.

Thanks

genotype population-genetics haplotype phase

• 3,224 views • link

updated 4.3 years ago by Ram

• written 11.5 years ago by evo_genomics •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Can iHS and XP-EHH be applied to targeted sequencing data?
written 1.1 years ago by slzr_ •

Hi everyone, I’m working with a dataset of samples from three different populations, sequenced using targeted amplicon panels covering 48 genes. Although most iHS and …
xpEHH
written 5.4 years ago by dominik.lagler •

Hello everyone, for my PhD i performed an EHH and an iHS for a certain candidate region (via subsetting all SNPs on that chromosome to …
the XP-EHH instruction
written 8.1 years ago by Victor •

Hello, I am trying to get the XP-EHH values by using HP-EXX. (https://github.com/joepickrell/xpehh) . I only have map and ped plink files in two populations. …
Genome-wide scans for selection using non-model organisms
written 9.3 years ago by aberry814

I have un-phased genome-wide SNP data from 150 samples of a diploid, non-model organism representing a single population. I am looking for a pipeline that …
CYP2D6 haplotype reconstruction
written 9.4 years ago by khn

Hello, I am trying to reconsturct haplotype of CYP2D6, using PHASE2.1.1 after GWAS. I know that there are limitations to reconstruct for CYP2D6 just from …
on going positive selection analysis using statistics IHS
written 9.5 years ago by qwzhang0601

I calculated the IHS statistics (the method is desribed in "A Map of Recent Positive Selection in the Human Genome". DOI: 10.1371/journal.pbio.0040072). This statistics measures …
Can I apply ihs/ehh on snp?
written 11.5 years ago by evo_genomics •

I am new in population genetics. I am working on a coding region of Human gene. I have found 5 human specific substitutions out of …
Cross population tests for detecting signals of positive selection: Rsb or XP-EHH?
written 11.5 years ago by JMR

<p>I am working on dense genotype data trying to detect signals of positive selection.</p> <p>I recently estimated the iHS statistic of my sample using the …
Positive selection in admixed human genomes using EHH tests are realiable?
written 11.7 years ago by JMR

I am trying to identify signals of positive selection in an admixed sample, using genome-wide SNP data. For a start, I want to use Extended …
Where Do We Use Haplotype Reconstarction Result?
written 13.6 years ago by mary

<p>Dear all</p> <p>I have studied Linkage Disequilibrium on genotyped data (SNP chip) from 6 month ago. I read in many article that they did haplotype …