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• Haplotype Construction Using Phase Version 2.1
  It would be great if someone can help with Haplotype construction using PHASE version 2.1. I have...
• From PHASE to HaploView
  I finally built a PHASE input file (.inp) and my analysis was executed successfully. Now I have ...
• Haplotype Analysis of Phased Genotype Data
  Dear All, I am a complete novice to haplotype analysis and I spent days to search for a tutori...
• 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...
• 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...
• Haplotype phasing and imputation in Beagle 5.1
  Dear members, Anybody elaborate on the steps for **haplotype phasing and imputation in Beagle v5....
• How To Prepare The Input For The Germline Software For The Inference Of Ibd Patterns
  Hello I wanted to use the program GERMLINE for the inference of IBD patterns and then DASH for t...
• hapcut2 output and figures
  I have run Hapcut2 and have a VCF file. I can't see in the VCF where it has assigned the snp to o...
• From Phased File Formats To Vcf
  I need to convert phased data (map and haplotype file) from the Hapmap Phase II data to vcf files...
• Ka/Ks Ratio To Detect Selection (Nonsynonmous To Synonymous) In Dnasp
  hello everyone, I have sequencing data for my gene from >2000 individuals. I want to look at ...
• Case-control phased Haplotype logistic regression on SPSS
  I have phased haplotypes based on 13 SNPs, which generated 17 unique haplotypes on my case-contro...
• Extracting haplotypes from phased vcf file
  I have a phased genotype VCF file(i.e haplotype in vcf format). I am interested only in the haplo...
• Convert vcf files with phased genotypes to standard haplotype format
  Hello, I have a set of .vcf files with phased genotypes that I would like to convert to standard ...
• How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI
  How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI? VCF file...
• Phasing with Beagle
  Good afternoon, I'm working with a lizard species and we did a target capture sequencing for the ...
• Convert Phase Output To Plink
  Hi guys, I was wondering whether there is a way to convert the output files of PHASE to plink fo...
• help with PHASE 2.1 program
  Hi all I'm having some troubles to run the program PHASE 2.1, starts to run but then suddenly sto...
• 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...
• Haploview (haps format)
  Hi How can I convert phase format (output beagle) to haps format (input Haploview)?
• Phasing using SHAPEIT
  Hello, I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) an...
• use gatk phased vcf as input file of HapCut2
  I am new in sequencing analysis and would like to do haplotype blocks from the result of WGS. But...
• Parahaplo Software For Haplotype Phasing And Imputation
  Hi All, Have you ever try paraHaplo software (http://www.scfbm.org/content/6/1/10) ? I would lik...
• Phasing Confidence Values using Shapeit2
  Hello everyone, I have 12 singleton WGS samples that I am trying to phase using Shapeit2 using ...