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• How To Convert A Multisample Vcf To A Format That Can Be Loaded In Haploview?
  How can I convert a multisample vcf file to a format that can be loaded in Haploview? I have WGS...
• Is there a tool or method for phasing a VCF based on an already phased BAM?
  I have some BAM files where the reads are phased, such that each read belongs to haplotype 1 or 2...
• converting vcf to haploview with keep phasing
  dear all after haplotype phasing with beagle v4, now i have vcf (phased file data) file. but i d...
• list of samples who carry specific haplotypes
  Hi all, I am currently doing haplotype analysis using haploview. Haploview gives me several hapl...
• Plink 1.9 haplotype blocks with not phased data
  Hi! I am trying to calculate haplotype blocks with PLINK 1.9 command `--blocks`. My data is **un...
• 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 use 1000 Genomes data for LDheatmap package in R
  I am trying to visualize LD blocks within 1Mb flanking a SNP. And I don't want to use Haploview b...
• Phased - Unphased genotypes
  Hi, I would ask if someone could clarify me the concept of phased/unphased genotypes. In the fir...
• Identify haplotype block using unphased genotype data
  I have some SNP array data of non-model species. I want to identify haplotype blocks using Hapvie...
• Imputating individual haplotype phase w/o Plink
  Hi, I have some unphased SNP (6 SNPs all from same gene) data from a human study, and know that s...
• How To Reconstruct Haplotypes And Visualize Them In Haploview
  Dear all I genotyped data from 1500 animals by 50K chips, and now I want to use haploview for bl...
• How does plink calculates linkage disequilibrium (r2) in unphased data?
  Hello when I pass a vcf file to plink, it can calculate the linkage disequilibrium (r2) even tho...
• Haplotype Block Database
  Hi, I'm trying to find a database of precomputed haplotype blocks (really interested in just th...
• 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...
• Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
  As this page explains, phased genotypes are alleles-order-sensitive. I assume that the order of ...
• How to convert Plink's ped/map files into nexus format?
  Dear all, I need to make a phylogenetic network using unphased Illumina genotyping data stored in...
• from phased SNPs to haplotype blocks (or phase sets)
  Hi all, I have successfully **phased a set of heterozygous SNPs** (only one sample) via the **EAG...
• How does haploview generates Haplotypes from primary genotype data
  Haploview can get you different block, haplotypes, just from SNPs sequences. I want to know which...
• SHAPEIT allele encoding
  My goal is to do phasing using shapeit2 (I don't have haplotype reference panels) and I have .ped...
• How to determine parent of origin of phased variants when all members are het
  I'm a little confused on the format of phased variants in a VCF file. I was under the assumption ...