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• Polygenic Risk Score PLINK
  Hi, I have got my .assoc file with Odd Ratio for each SNP. Now I need help to understand how to ...
• Info Score > 1 Plink?
  What does an info score > 1 mean? I thought all scores should be between 0 and 1. Info score c...
• Calculation of Mentha Score
  What is mentha score ? How can we calculate Biological Stability Index score for a gene dataset?
• Base file of PRSice software
  I am using PRSice software for Polygenic risk score calculation of complex diseases like Type 2 D...
• How do BOLT and SAIGE calculate LD?... with PLINK LD?
  When you run a PLINK GWAS, you run PLINK LD on the significant hits. How is LD calculated for ot...
• How to calculate IBD for different ethnicity using plink
  I have a multigenome vcf file with samples from different ethnicities. I have converted this file...
• How is it possible to create a .fam file with PLINK with phenotypic data (for GEMMA)?
  I want to use GEMMA to calculate association mapping. But I need a .fam file to run the GEMMA pro...
• The Calculation of Enrichment Score and Group Enrichment Score in gene set enrichment analysis DAVID?
  I am new to bioinformatics, I'm wonder is there a Calculation of Enrichment Score (ES) and Group ...
• Extracting imputation (INFO) quality scores for specific SNPs from VCF files
  Would be very grateful for help. I have a VCF.gz file for imputed SNP data. I know for a fact t...
• Peak Score Calculation in Homer
  Hi, How is Peak Score calculated in Homer (http://homer.salk.edu/homer/ngs/index.html) ? Thanks.
• Plink scoring function mechanism
  To use `--score ScoreFile` function, in `ScoreFile`, we need SNP ID, effect allele and effect siz...
• update fam file VCF -> plink bfile
  I have a large VCF (WGS >7000 samples) that I converted to plink bfile with this command ...
• minimum snp number from set in LD
  ok I have run things through plink and I have a list of SNPs from a file. I want to know how much...
• How plink calculates meta-analysis
  I am trying to find the logic/calculation what is used in plink to calculate the meta analysis wh...
• How Is The Score And E-Value Calculated In Blast Outputs
  Hi! I am working on a BLAST similar tool and wanted to implement the Score (raw Alignment score)...
• Question about PLINK allelic scoring (PRS)
  Currently, I'm trying to use PLINK Allelic Scoring (plink --score). And it generates four output...
• How is the Bolt LMM INFO Score calculated?
  Hi I am trying to find what exactly does the INFO score from the results of [Bolt LMM][1] measur...
• 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...
• Simulating data PLINK/ GCTA
  Hi, I am new in plink and gcta. With simulated data, I need to construct polygenic score and the...
• score parameter in multimiR
  Hello everyone, Can anyone please guide me about the scoring param...
• Correlation of PRS obtained by plink and PRSice
  I want to know why the correlation of PRS obtained by plink and PRSice is low. Firstly, I used pl...
• How to run an identity-by-descent calculation on plink with a p-value threshold?
  I've already run an SNP filter using plink on map and pedigree files, now i want to run IBD with ...