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• loadling bcf2 file in plink
  I am using bcftools to save a bcf2 file (chr22.bcf2) for a later analysis using plink. bcfto...
• merging GWAS data sets in Plink, error message: merge-equal-pos failure. Variants 'rs___a' and 'rs__b' have the same position, but do not share the same alleles
  Hi, I am trying to merge two GWAS data sets in Plink.  Apparently there are multiple variant ids...
• What are the major differences between plink and plink2?
  Hi, I was running plink(1.9) tool to create bed file (`plink --file inputfile --make-bed --noweb ...
• PLINK2 recode ped flag issue
  Hi, I am trying to covert .ped and .map files to a VCF file using plink2, as in the examples bel...
• GATK SelectVariant and Separation of Variants
  Hello cheerful bioinformaticians :) I have a problem about GATK SelectVariant tool. I have a VCF...
• How to process Plink2 --score across chromosomes
  I'd like to run the --score flag across chromosomes. I tried this syntax: # PBS -t 1-22 plin...
• ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
  When running the command with deeptools: DIR=~/TESTING/day2_fos20_intersection computeMa...
• Plink2 error: Skipping --glm regression on phenotype 'PHENO1' since variance inflation factor for covariate 'COVAR1' is too high.
  I am calculating the SNP effect with plink2, I used the external phenotype instead of inside the ...
• 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...
• R: read.plink Error
  Using `read.plink` from `snpMatrix` I use following command to read bed file in R: read.pli...
• Fewer tokens than expected error in Plink when using --filter
  Hello, I am working with .bed .bim and .fam files from the Drosophila Genetic Reference Panel (ht...
• Full-stop/period as SNP identifier in BIM file causes error in Plink v1.9 --read-freq command
  In the example shown below, you see that certain variants have a full-stop/period instead of an i...
• Simultaneous vs sequential marker filters
  Hello! Could somebody please clarify why imposing the marker filters step-by-step vs all at once...
• PLINK Merge error: File write failure
  Hi,  I am trying two merge 1000Genomes with another already merged data set using PLINK 1.9. I a...
• Beagle VCF header issue
  I've received a bed/bim/fam set of data that I'm trying to use for imputation, and I'm having iss...
• Best way to convert VCF to PLINK file format and merge chromosomes?
  I am trying to convert the 1000G genotypes into plink format so I can try to run a PCA.  I used ...
• How to recode VCF from bed bim and fam files in plink with filter?
  I am trying to create a vcf in plink. Currently as a practice run I have tried this with just loo...
• PLINK2 association study using covariate regression model
  Hello all, I'm using PLINK2 to do assication study in a case-control trait. I have 4 covariates....
• bwtool matrix error - invalid signed integer
  Hi all, I am using bwtool to make a matrix for footprinting a TF using a BED file I generated wi...
• Error With Unifiedgenotyper With Option -Glm Both With Gatk During Variant Calling
  Hi, I am using the below command for calling the raw variants using GATK(GenomeAnalysisTK-2.3-4-...
• Plink - resolving heterozygous haploid genotypes if an XY chromosome is already assigned in GWAS
  There is a previous biostars post that deals with the use of plink2's --split-x flag to handle ca...
• 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 ...