# \#gcta **URL:** https://isgw-forum.colorado.edu/tag/gcta/1.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) --- ## [Comparing LDSC, GREML, and HE Heritability](https://isgw-forum.colorado.edu/t/comparing-ldsc-greml-and-he-heritability/884)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:24pm UTC](https://isgw-forum.colorado.edu/t/comparing-ldsc-greml-and-he-heritability/884 "2026-06-10T14:24:58Z")
Should we check if h2 from sum stats via LDSC are the same/similar to h2 from HE regression/GREML? Replying to “Should we check if h2 from sum stats via LDSC are …”: If you have access to suitable data to check that,… --- ## [Twin Samples and PRS](https://isgw-forum.colorado.edu/t/twin-samples-and-prs/863)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:31pm UTC](https://isgw-forum.colorado.edu/t/twin-samples-and-prs/863 "2026-06-10T13:31:46Z")
When working with twin simples and PGS, what is the preferred approach for accounting for relatedness? Is it sufficient to model family structure using a random effect (e.g., 1 | FAMID), or is it preferable to account fo… --- ## [Asking questions about BLUP](https://isgw-forum.colorado.edu/t/asking-questions-about-blup/828)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 0\ **Last updated:** [June 9, 2026, 2:34am UTC](https://isgw-forum.colorado.edu/t/asking-questions-about-blup/828 "2026-06-09T02:34:11Z")
Hi Professors, “I have a general question regarding ‘Part 3: Conventional methods for PGS prediction.’ On page 8, it states that BLUP is a linear mixed-effects model. Is this mixed model the same as the model used in GC… --- ## [GCTA for big datasets and sequencing data](https://isgw-forum.colorado.edu/t/gcta-for-big-datasets-and-sequencing-data/754)
**Author:** [@carmen.ramoser](https://isgw-forum.colorado.edu/u/carmen.ramoser)\ **Replies:** 3\ **Last updated:** [June 3, 2026, 12:21pm UTC](https://isgw-forum.colorado.edu/t/gcta-for-big-datasets-and-sequencing-data/754 "2026-06-03T12:21:29Z")
Thank you for the very interesting practical despite the problems. Loic mentioned that GCTA should not be used for big datasets. I wanted to ask if it is possible to use it for a dataset of 70.000? As I understood the t… --- ## [Selective samples and GCTA](https://isgw-forum.colorado.edu/t/selective-samples-and-gcta/752)
**Author:** [@henrik.dobewall](https://isgw-forum.colorado.edu/u/henrik.dobewall)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 1:59am UTC](https://isgw-forum.colorado.edu/t/selective-samples-and-gcta/752 "2026-06-03T01:59:19Z")
We talk about unmet assumptions like assortative mating, height education etc. But as we are working with selective samples, e.g. due to volunteer bias, our samples are usually more educated, healthier, older, more urban… --- ## [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 … --- ## [Installation problems with GCTA in mac system](https://isgw-forum.colorado.edu/t/installation-problems-with-gcta-in-mac-system/380)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 1\ **Last updated:** [July 11, 2022, 9:20pm UTC](https://isgw-forum.colorado.edu/t/installation-problems-with-gcta-in-mac-system/380 "2022-07-11T21:20:58Z")
Hi, I don’t know whether this is a good place to ask about the question of the installation of GCTA. I have tried to run GCTA and LDSC on my own laptop which is macbook with OS system for the practical. However, it seem… --- ## [Some quick questions, just wondering if I can have a chance to ask these questions after the workshop](https://isgw-forum.colorado.edu/t/some-quick-questions-just-wondering-if-i-can-have-a-chance-to-ask-these-questions-after-the-workshop/366)
**Author:** [@huynguyenacademia](https://isgw-forum.colorado.edu/u/huynguyenacademia)\ **Replies:** 2\ **Last updated:** [June 20, 2022, 11:46am UTC](https://isgw-forum.colorado.edu/t/some-quick-questions-just-wondering-if-i-can-have-a-chance-to-ask-these-questions-after-the-workshop/366 "2022-06-20T11:46:34Z")
Dear Lecturers and Tutors, Thank you for your excellent lectures and tutorings. I still have three quick questions. Though workshops ended, I just wonder if I can ask these questions: In slide 13 (Day 8, pdf on Estim… --- ## [Error message run in SSH for day 7 stretch goal 1 GCTA practice](https://isgw-forum.colorado.edu/t/error-message-run-in-ssh-for-day-7-stretch-goal-1-gcta-practice/356)
**Author:** [@anonymous3](https://isgw-forum.colorado.edu/u/anonymous3)\ **Replies:** 2\ **Last updated:** [June 16, 2022, 11:17pm UTC](https://isgw-forum.colorado.edu/t/error-message-run-in-ssh-for-day-7-stretch-goal-1-gcta-practice/356 "2022-06-16T23:17:33Z")
Running below coding in SSH for day 7 stretch goal 1 GCTA practice, I got an error message. gcta64 --pheno ozht.phen --qcovar ozht.prs1.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS1.ACE --reml --reml-est-f…