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• Haplotype Phasing with Shapeit2
  Hi everyone, I am anew in haplotype phasing. I have 14 WGS individuals data from one human popu...
• Does HaploView perform phasing?
  I have super newbie questions. As far as I understand HaploView can display a PED file containin...
• Calculating association with outcome variable and Phased Haplotypes
  I am trying to determine association between a set of haplotypes (2 or 3 marker SNPs) with a clin...
• Genotype phased and unphased
  Can anybody tell help me explain the difference between 0/1 and 0|1 genotype when, we do snp anal...
• Which software can be used to extend the partially phased vcf from several different individuals (samples) to get an extend length haplotype?
  I have vcf files which has partially phased genotypes as different blocks. These variants and pha...
• transmitted and untransmitted alleles
  Sorry the question seems very basic, yet I coulnd't find it on google. When browsing through the ...
• Statistical Genetics - What information is required for haplotype phasing in a novel, admixed population?
  Let's say there is a population that has never been sequenced before and has experienced varying ...
• Expression to tell bcftools consensus to treat phased heterozygotes differently from unphased?
  **tl;dr: I want help writing an expression for bcftools consensus to tell it to put Ns in my hapl...
• Where Do We Use Haplotype Reconstarction Result?
  Dear all I have studied Linkage Disequilibrium on genotyped data (SNP chip) from 6 month ago. I ...
• What Are Phased And Unphased Genotypes?
  As the title implies, "what are phased and unphased genotypes?" I am playing with 1000 genomes da...
• Non-overlapping genomic haplotype blocks
  Hi All,   I am trying to search list of non-overlapping haplotype blocks for CEU population (or...
• Estimating Haplotypes
  Hypothetical question just to illustrate what I'm trying to do: A small gene "FOOBAR" on human c...
• Split phased haplotypes of same person coming from same parents
  Hi, I have phased haplotypes of two samples from same person. However, since they are coming fro...
• mach1 phasing reference Haplotypes file(s)
  mach1 has an option "-h" to specify reference haplotypes for phasing, but I am having trouble fin...
• Haplotype resolving (phasing) from BAM file
  Hi all, I have a question about what I first thought would be a trivial task. I would like to re...
• Question: How to tell the haplotypes used by minimac to determine dosage for a specific site?
  I am using a 2-step approach to imputation: phasing with hapiur, followed by imputation with mini...
• how can I make input file for Haploview from Output files of inferred haplotypes by fastPHASE?
  Dear all I am doing LD analysis and selection signature on 50k snp data of cattle. For the analy...
• How To Visualise The Flow Of Genotypes/Haplotypes Through The Pedigree?
  Hi can any one recommend any software for working with phased VCF files? I've a complete 4 gener...
• Phased - Unphased genotypes
  Hi, I would ask if someone could clarify me the concept of phased/unphased genotypes. In the fir...