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• 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...
• Combining inhouse data with 1000 genome for PCA
  For PCA analysis, I have common coordinates between Inhouse exome data and 1000 Genomes data (Pha...
• 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...
• How to phase a vcf file
  Hi I want to Phasing VCF file. But I do not know how this work is done? What software is requir...
• How to convert a raw vcf to a phased vcf
  Hi, I generated a vcf file called variants using Freebayes. Further, I would like to perform nor...
• Convert BED(UCSC) to VCF
  I am using liftOver to convert hg19-hg38. I made BED file from VCF to run liftOver. How can I con...
• 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 ...
• Convert IMPUTE2 to VCF while keeping phase information
  Hi,   I have imputed genotypes using the IMPUTE2 software. Now I need to convert my IMPUTE2 form...
• Phasing Confidence Values using Shapeit2
  Hello everyone, I have 12 singleton WGS samples that I am trying to phase using Shapeit2 using ...
• 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...
• How to convert vcf to impute2 format?
  Hi, i want to phase my data in vcf format using impute2's "-phase" option. So i tried to convert ...
• Break the VCF file to 5 populations
  Hi all, My final VCF file contains 5 populations, and I want to break it into 5 populations firs...
• Merge phased SNP variants to haplotypes? And is vcfallelicprimitives reversible?
  Is is possible to create a VCF file were phased variants are merged to haplotypes? Say I have a ...
• 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...
• VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased
  I have an excel spreadsheet I'm trying convert to VCF File. I've got most fields right but I can...
• Extract unphased genotypes from vcf file and convert to 012 matrix
  I have a vcf file in which I want to extract the genotypes and convert them into a 0,1, 2 matrix....
• Problem with Haploview loading of files from latest (Sept 15-17 2014) update to phase 3 release of 1000 Genomes data
  I am having all kinds of trouble with loading files from 1000 Genomes into Haploview. This seems ...
• 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...