Similar posts • Search »

• liftover using GWAS summary data and PLINK binary files (bed/bim/fam)
  Hi,  I have a GWAS summary data (chr, snp, bp beta, se etc.) file based on the 1000G Aug 2010 10...
• Plink calculator for calculating pairwise LD
  Hi, I have list of snps in vcf format. Can p link LD calculator be used for pairwise LD calculat...
• How could I input a folder of bed, bim, fam files with different chromsomes to plink as --bfile mydata?
  Hello, I am new in LD analysis. I have a snp list from different chromosomes and a list of region...
• Calculating LD between specific alleles even if they are not the minor alleles
  Hello, I have a list of SNPs across several populations. Because I am dealing with transethnic d...
• how to use plink to get all the SNP LD score > 0.8 in matrix format?
  I am a freshmen with plink. I downloaded the 1000 genome phase 3 data and try to get all the snp ...
• How To Calculate All Ld Results For 1000G Raw Genotypes?
  Hi everyone, I am using the raw 1000G genotypes 20101123 release version to calculate all the LD...
• PLINK extracting more variants than in file when calculating LD (with --extract modifier).
  EDIT: I tried the same command with PLINK 1.07 and it works fine, but significantly slower. Anoth...
• Ld Analysis
  Dear Friend I have a population with 1066 bulls that just sire was genotyped by Illumina Bovine ...
• ld matrix in plink
  I am using the below command to generate an LD matrix in plink plink --r2 --bfile bfilename...
• formula to calculate LD in plink
  Could any kind of person tell me the formula to calculate Linkage disequilibrium in the plink. Th...
• Consistency of LD in the two populations
  I have two population. I used PLINK for calculating LD. The consistency of LD in the two populati...
• How to calculate the LD from a list of SNPs using plink
  Hi， I have a list of SNPs (with marker RS id) in a .txt file. Beacuse we don't have the .ped f...
• No output estimating LD between SNPs in VCF using PLINK
  I want to estimate the LD (in r2) between two snps present in a VCF file. However, even if the va...
• Specify A Customed Output File For Ld Calculation Using Plink
  Hi, friends, Recently I am using PLINK software to calculate the LD among a given SNP set. The s...
• PLINK: Compute LD from list of SNPs using 1000 Genomes
  I have a list of SNPs. I'd like compute the r-squared values to remove any SNPs that are in linka...
• Using Plink to calculate LD between loci on different chromosomes
  I'm trying to calculate LD between loci on different chromosomes using plink on the 1000 genomes ...
• Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
  I want to calculate markerwise Weir And Cockerham Fst for certain differentiating markers. I have...
• Creating Binary file (*.bed, *.bim, *.fam file) from 1000GP LEGEND file
  Hi All, I have the file "1000GP_Phase3_combined.legend". I want to create a binary (*.bed, *.b...
• Estimating LD score in PLINK
  LD score is defined as the sum of LD r2 between a variant and all the variants in a region. I wa...