# \#plink **URL:** https://isgw-forum.colorado.edu/tag/plink/8.md [Latest](https://isgw-forum.colorado.edu/latest.md) · [Categories](https://isgw-forum.colorado.edu/categories.md) · [Tags](https://isgw-forum.colorado.edu/tags.md) --- ## [GWAS lectures](https://isgw-forum.colorado.edu/t/gwas-lectures/778)
**Author:** [@Shal](https://isgw-forum.colorado.edu/u/Shal)\ **Replies:** 1\ **Last updated:** [June 5, 2026, 2:20pm UTC](https://isgw-forum.colorado.edu/t/gwas-lectures/778 "2026-06-05T14:20:24Z")
Hi Abdel, While going through the course lectures, I had a few questions about the GWAS workflow. Apologies if some of these are very basic. PCA and covariate file for PLINK When conducting a small GWAS in PLINK, … --- ## [Nuanced use of PCs with GRMs](https://isgw-forum.colorado.edu/t/nuanced-use-of-pcs-with-grms/816)
**Author:** [@rbhowmic](https://isgw-forum.colorado.edu/u/rbhowmic)\ **Replies:** 0\ **Last updated:** [June 5, 2026, 2:04pm UTC](https://isgw-forum.colorado.edu/t/nuanced-use-of-pcs-with-grms/816 "2026-06-05T14:04:43Z")
We had a helpful discussion on the selection of covariates for GWAS analysis on Day4. While GRMs capture genetic relatedness, including PCs is also recommended to account for overall genotype similarity across population… --- ## [File format](https://isgw-forum.colorado.edu/t/file-format/763)
**Author:** [@Shal](https://isgw-forum.colorado.edu/u/Shal)\ **Replies:** 3\ **Last updated:** [June 3, 2026, 9:42am UTC](https://isgw-forum.colorado.edu/t/file-format/763 "2026-06-03T09:42:39Z")
Do genotype companies like Illumina provide a file that is PLINK-friendly, or do we convert the raw genotype file into .bed/.bim/.fam ? Thanks Shal --- ## [Question about SNP-heritability and alleles in PLINK](https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755)
**Author:** [@Shal](https://isgw-forum.colorado.edu/u/Shal)\ **Replies:** 0\ **Last updated:** [June 2, 2026, 10:55am UTC](https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755 "2026-06-02T10:55:34Z")
Hi Loic, Thank you again for the wonderful session yesterday. I have a question about heritability. When we have a large sample size, is it standard practice to use PLINK to estimate SNP-heritability in a set of unrela… --- ## [HE vs REML estimator in GWAS](https://isgw-forum.colorado.edu/t/he-vs-reml-estimator-in-gwas/648)
**Author:** [@Ralph\_Porneso](https://isgw-forum.colorado.edu/u/Ralph_Porneso)\ **Replies:** 1\ **Last updated:** [May 20, 2024, 12:07am UTC](https://isgw-forum.colorado.edu/t/he-vs-reml-estimator-in-gwas/648 "2024-05-20T00:07:13Z")
Hi, Are there some good references or is there someone who knows the scale of the difference in computation between REML and HE to estimate the variance components in a mixed effects model, say in GCTA fastGWA? I have … --- ## [Transmitted and non-transmitted alleles](https://isgw-forum.colorado.edu/t/transmitted-and-non-transmitted-alleles/644)
**Author:** [@michek18](https://isgw-forum.colorado.edu/u/michek18)\ **Replies:** 0\ **Last updated:** [April 23, 2024, 12:33am UTC](https://isgw-forum.colorado.edu/t/transmitted-and-non-transmitted-alleles/644 "2024-04-23T00:33:10Z")
Hi, I’ve been revisiting the lecture on “Estimating Intergenerational Transmission” by Jared Balbona. I am confused about the influence of paternal and maternal Familial Environment (FE; Fp and Fm). Based on Jared’s exa… --- ## [About QC of data from different microarrays](https://isgw-forum.colorado.edu/t/about-qc-of-data-from-different-microarrays/504)
**Author:** [@Bruna](https://isgw-forum.colorado.edu/u/Bruna)\ **Replies:** 1\ **Last updated:** [March 7, 2023, 9:54pm UTC](https://isgw-forum.colorado.edu/t/about-qc-of-data-from-different-microarrays/504 "2023-03-07T21:54:51Z")
Is that ok to merge datasets from different microarrays (for example, using bmerge plink command) before imputation? What are additional QC steps to check the quality of the merged dataset (e.g. flip issues)? What if the… --- ## [Day1 QC session - practical links](https://isgw-forum.colorado.edu/t/day1-qc-session-practical-links/462)
**Author:** [@daniel.howrigan](https://isgw-forum.colorado.edu/u/daniel.howrigan)\ **Replies:** 0\ **Last updated:** [March 6, 2023, 5:22pm UTC](https://isgw-forum.colorado.edu/t/day1-qc-session-practical-links/462 "2023-03-06T17:22:50Z")
3 ways to view the QC practical session: Qualtrics website with full QC script: https://ucsas.qualtrics.com/jfe/form/SV\_eWpdYL7srw7Cy6W Workshop server access to full QC script: less -S /faculty/daniel/2023/QC/QC\_pra…