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• Plink allele scoring output
  Hello, I am using PLINK2 to create a profile score and am confused to what the output represent:...
• SNP scoring using PLINK
  I am using the --score command in plink to estimate profiles for individuals based on an allelic ...
• How to convert PLINK file (map, ped) to haplotype file for XPEHH application
  Hello I am the first year PhD student in University . Basically, I'm new to PLINK (obviously)...
• Un-weighted Polygenic Risk Score in plink
  Dear all I am using –score function in plink to generate polygenic risk score. Against the –score...
• How plink calculates the INFO scores ?
  The summary file from plink's `--dosage` command has a column 'INFO' with values about the imputa...
• update fam file VCF -> plink bfile
  I have a large VCF (WGS >7000 samples) that I converted to plink bfile with this command ...
• PLINK - Obtaining polygenic score
  Hi, I am trying to obtain in PLINK the polygenic scores of a sample of individuals. I simulated ...
• PLINK Error: No valid entries in --score file.
  Hi all, When I use plink to run `--score` function I got an Error: > No valid entries in --s...
• Obtain A1 and A2 alleles from plink output
  I'm trying to convert plink output to the [`.sumstats` format][1] for use with LD score regressio...
• Plink scoring function mechanism
  To use `--score ScoreFile` function, in `ScoreFile`, we need SNP ID, effect allele and effect siz...
• Question about re-coding SNPs in PLINK
  Hi there, I'm working on a blood pressure genetics project and have got a bit stuck. I am trying...
• Info Score > 1 Plink?
  What does an info score > 1 mean? I thought all scores should be between 0 and 1. Info score c...
• what is 0 in the plink .bim file under allele1/2 column?
  Hello, I have a bfile data that contains zero "0" in the allele column in .bim file. Both allele...
• 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...
• Illumina final report file to PLINK
  Hi everyone, I have to work with some GWAS data from a previous collaborator and I have only the...
• Forcing A1/A2 alleles in PLINK in a VCF phased file
  I have a phased VCF file and I need to change the alleles of the SNPs so that the alleles coded a...
• Is it possible to specify a reference allele while computing LD in Plink?
  Hi,   I am using methods of analysis where it is necessary that the LD and effect sizes are com...