plink2-users - Google Groups
Feb 28, 2026 · - Major release announcements (including major bugfixes) are posted to the plink2-announce Google group. They will still be cross-posted to plink2-users.
How do I merge several binary files from separate samples into a single ...
May 27, 2024 · So, I am asking plink2 to generate a single file using the Plink1 format, but plink2 is looking for a .psam file, which is not there. Also, I am not clear on what the file for --bfile should be …
--score for polygenic risk score with PLINK 2.0 - Google Groups
Sep 4, 2018 · I was wondering if the --score function works differently in plink 2.0 than plink 1.9 with their respective binary files (.pgen, .pvar, .psam vs. .bed, .bim, .fam). I have a text file formatted as a …
Input filtering based on imputation score (R2) - Google Groups
Jan 25, 2018 · I was wondering, whether Plink 2 is capable of filtering SNPs from vcf-files based on imputation score (R2)? Technically documentation says in the Input filtering-section that for example …
Troubleshooting multallelic variant merging issue - Google Groups
Oct 18, 2023 · I want to recode the IIDs of imputed data .bgen files into two different filesets, and merge these (working on eye-level analyses with Regenie). As I'm only interested in dosages, I've …
The fast way to remove all the multiallelic SNPs in plink2
Mar 13, 2020 · plink2 will have a function to join this type of multiallelic variant back together soon. For now, you'd use "--export bcf", use bcftools norm to do the job, and then --bcf to retrieve the results.
LD calculation in plink2 - Google Groups
Jan 2, 2024 · Does this mean that plink2 outputs the LD between the reference alleles that are specified by the .pvar file? Also, is it correct that for "--r2-unphased" it is irrelevant if its reported with respect to …
treat chrX as autosome - Google Groups
May 1, 2024 · Maybe to provide a bit of background: I know many studies that used plink1.9 or plink2 to do an autosome-wide PCA in my target species, by circumventing the problem of plink of being …
Question about multiallelic variants in plink 1.9 and 2
Jan 15, 2020 · I'm currently writing a simple vcf to bed conversion pipeline on cromwell. I need to use a mix of plink1.9 and plink 2 since the multithreading comes in handy, but plink2 doesn't support - …
What is the A1 and A2 in the GWAS output? - Google Groups
Avni Kaur Apr 12, 2024, 7:17:25 AM to plink2-users Dear Plink users, I have a very quick question regarding what is A1 and what is A2 for running a meta-analysis. If this is the output from my GWAS …