I have genotype files in plink format (.bed, .fam and .bim) and I would like to know how can I convert it to .pgen format?

I have a summary statistic file which has the the following columns Column Description ID_37 Variant ID (GRCh37) Chromosome Chromosome number Position_b37 Position GRCh37 Other_allele …

Trying to calculate MAFs for a VCF file with 40 samples, tried PLINK and PLINK2 (--freq) and the output is something like: chr | rs …

I'm working on some summary stats which doesn't have a MAF column. What is the best way to impute MAF from the European reference panel? …

I have a list of rs IDs (>1000) and I would like to know how I can get the chromosome number and the position? TIA

Hello, I am using the UCSC lift over tool and the associated chain to lift over the results of my GWAS summary statistic file (a …

I know that METAL can perform meta-analysis on GWAS summary statistic files, so for Meta-GWAS summary statistic results, can also be used for METAL's input …

Hello, Please I would like to merge one same column to multiple different files. Those files have the same structure but from different samples and …

I have a whole genome SNP data for few hundred patients stored in SAS datasets and I would like to know, How I can filter …

<p>Say I have 100 SNPs from literature associated with certain phenotype/trait - I would like to know how can I pick up the few important …