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GWAS, quantitative traits
quantitative traits gwas written 6 days ago by Adarsh Kuamr • 40
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merging multiple chromosomes in a single file
gwas prs plink snp written 6 days ago by bigfoot • 0 • updated 6 days ago by chrchang523 ♦ 4.9k
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PLINK2 and data split by chromosomes
genome gwas prs plink snp written 6 days ago by bigfoot • 0
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Do we have to use a covariance (at quantitative scale) that is a normal distribution in linear regression when running a GWAS
gwas linear regression written 8 weeks ago by wenqianglongli • 10 • updated 6 days ago by Biostar ♦♦ 20
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how to study genetic correlation between two traits
genetic correlations gwas genotype written 8 days ago by lilingjoyo • 30 • updated 8 days ago by genomax ♦ 65k
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Polygenic Risk Score analysis using PRSice
genome gwas next-gen snp sequencing written 12 days ago by sofie_carolina • 20
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Infer pedigree from Kinship coefficients
gwas kinship written 12 days ago by landscape95 • 160
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PRSice PRS calculation warning Mismatched SNPs. Is it due to using multi-covariate for SNP effect size?
prsice gwas written 12 weeks ago by landscape95 • 160 • updated 14 days ago by Sam • 2.3k
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PRSice threshold result is not as expected
prsice gwas written 11 weeks ago by landscape95 • 160 • updated 14 days ago by Sam • 2.3k
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Fitting year or location as a covariate in GAPIT
gwas gapit R written 17 days ago by artolkamp • 30
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Why there is no beta of SE output in some meta GWAS results?
gwas meta beta se written 19 days ago by lilingjoyo • 30
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108
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Error when doing gwas with hail
gwas hail written 4 weeks ago by barry_reeves • 0 • updated 21 days ago by Biostar ♦♦ 20
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Chromosome X GWAS in related individuals
gemma chromosome x related individuals gwas written 23 days ago by alesssia • 510 • updated 21 days ago by Kevin Blighe ♦ 41k
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Using PLINK to filter VCF files
vcf gwas plink written 2.8 years ago by Diego.Morales • 10 • updated 4 weeks ago by Kevin Blighe ♦ 41k
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LD filter for GWAS with plink
gwas linkage disequilibrium plink written 4 weeks ago by sonia.olaechea • 60
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Haploview cannot connect to HapMap Database
hapmap genome haplotypes haploview gwas written 4 weeks ago by novice_bioinformatician • 0
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Duplicates in plink files (same position, same ref allele but different A1 allele)
gwas plink snpchip written 2.8 years ago by Mamta • 410 • updated 5 weeks ago by Hasanga • 0
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122
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Strange behaviour of the NCBI remap API ?
ncbi assembly alignment genome gwas written 6 weeks ago by f.abbondanza94 • 0
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127
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Making a phenotype file in PLINK
gwas make-pheno plink phenotype data written 6 weeks ago by 123sanjanagupta • 0 • updated 6 weeks ago by genomax ♦ 65k
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Reference set of SNPs for SNP-pruning for PCA in GWAS
gwas pca pruning snp linkage disequilibrium written 6 weeks ago by pcsk9 • 0
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Inflated p-values from QQ-plot for Lasso GWAS regression coefficients
gwas written 6 weeks ago by madbadradscientist • 0
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Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
gwas written 6 weeks ago by michael.nagle • 100
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How to imporve the P threshold value in FarmCPU (GWAS)
farmcpu multilocus mlm gwas written 6 weeks ago by BioRyder • 160
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126
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News: GWAS course in Canada
gwas news written 7 weeks ago by carlopecoraro2 • 910
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Epistasis in GWAS loci, examples?
epistasis gwas R written 7 weeks ago by Floris Brenk • 890
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Trying to get 1001 population Arabidopsis genotype and SNPs data
R 1001_genomes arabidopsis gwas farmcpu written 8 weeks ago by ycth8 • 0
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Split on Manhattan plots for chromosomes 1, 9, 16 (GWAS)
genome gwas snp written 8 weeks ago by ivanovaos.09 • 0
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Get SNP information with association test with PLINK
gwas plink written 8 weeks ago by landscape95 • 160 • updated 8 weeks ago by zx8754 ♦ 7.1k
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Many 0 in ped file converted from vcf genomic data
vcf gwas plink snp written 8 weeks ago by shawn • 20 • updated 8 weeks ago by zx8754 ♦ 7.1k
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How to use qqman using own data?
gwas R written 9 weeks ago by nbe • 0
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