Apr 15, 2026 · - Major release announcements (including major bugfixes) are posted to the plink2-announce Google group. They will still be cross-posted to plink2-users.

Oct 30, 2023 · Hello! For my mathematical analysis of genomic data, I would be needing a pruned and phased data of 1000 human genomes.

Mar 3, 2025 · Please see the screenshot below from the PLINK2 tutorial. It seems that both --export vcf and --recode vcf work fine. Is there actually any difference between these two options?

Aug 14, 2023 · Q2: --pmerge-list seems to require at least two inputs, which makes sense regarding #1 above, but not #2. I've previously wondered if it shouldn't eventually allow single-input, just as a …

Dec 10, 2024 · Anyway, result is now consistent between plink2 and R logistf. The problem is that the covariates are just too strongly associated with the phenotype; but if you crank up the number of …

Aug 14, 2022 · I am working with a .bgen file. I initially carried out the GWAS on the entire chromosome and retrieved a list of SNPs and their positions. However, I wanted to then do a GWAS on certain …

Feb 15, 2024 · if I use " plink2 --write-covar cols=+phenos ", then I have to run this command twice, for males and for females separately, and then merge the two output phenotype files, and then finally …

Dec 29, 2021 · I'd like to predict the A disease response depending on individual's genotype, using effect allele (variants) Now, I have two files 1. One is variants summary statistics (rsid, position, …

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Feb 14, 2024 · Generic data management for your notion of half-missing call, which isn't even defined in either the VCF or BGEN specification, is even further outside plink2's scope than genotype …