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• Error in Plink testing SNPs with independent effects
  Hi, This is regarding a problem that i am facing with testing whether SNPs have independent effe...
• 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...
• Haplotype Reconstruction
  Dear Friends I am going to reconstruct haplotype block for linkage disequilibrium analysis , is ...
• Case Control Haplotype Association Test
  Hello, what is your favorite software for Haplotype Case-Control GWAS testing? Please do not ment...
• 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...
• PLINK Haplotype blocks estimation not working
  Hi, I am using PLINK to estimate haplotype blocks using Gabriel's method. I am using the followi...
• Haplotype Genotype (Two Haplotype Alleles) Estimation In Plink Or Any Other Software
  I am trying to construct haplotype genotype using PLINK (if not possible need to use other softwa...
• Plink: How to run a quantitative TDT with haplotype window?
  Dear readers, I am trying to run a quantitative TDT with haplotypes with the PLINK programme. I ...
• Is it possible to use haplotypes instead of SNPs for association testing with phenotypes?
  > We need to start thinking about genome analysis as haplotype reconstruction- not variant cal...
• Problems with PLINK on Mac OS X
  Hi I want to start to use PLINK on OS X (El Capitan). I follow the instructions to download and ...
• Do imputed variants tend to show weaker, stronger, or the same average association compared to genotyped variants
  I was thinking about haplotype association analysis recently. I was thinking that a lot of haplo...
• LD pruning and other QC before association analysis ?
  Hello, Usually we perform QC stuffs such as removing SNP with a low degree of MAF, LD pruning et...
• Unknown error message in PLINK association analysis
  I've encountered a novel error while running association analysis in PLINK. I input the following...
• How to run PLINK from a personal computer
  Hi! This is my situation. I recieved a file in impute2 version and I need to do a mendelian rando...
• Quantitative trait analysis
  I have couple of queries regarding QTL (Enzyme activity) association with genotypes  which I did ...
• Logistic regression with Plink - conditioning to SNPs
  Hi all, I’m seeking to interpret the results of a logistic regression analysis with Plink. I'm ...
• Set-based test - PLINK
  Hi, Plink documentation explains two options when running a set-based test analysis. HINT Two e...
• help needed about PLINK joint test (--tests)
  Hi guys, I'm trying to use PLINK to perform a 2-degree-of-freedom test to jointly test the main g...
• No Snps Within The Given Range For Plink Association Analysis
  When using the --from-bp --to-bp options in plink, what happens if there is no snp within the giv...
• PLINK: No difference in quantitative association tests in spite of different disease groups?
  Greetings everyone, I have been using (and really digging) PLINK for a while now, but there is a...