# Day 2 **URL:** https://isgw-forum.colorado.edu/c/isg-workshops-2026/day-2/31.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) --- ## [About the Day 2 category](https://isgw-forum.colorado.edu/t/about-the-day-2-category/742)
**Author:** [@JML](https://isgw-forum.colorado.edu/u/JML)\ **Replies:** 0\ **Last updated:** [May 26, 2026, 5:09pm UTC](https://isgw-forum.colorado.edu/t/about-the-day-2-category/742 "2026-05-26T17:09:07Z")
assumptions, QC, imputation, PLINK and R basics, phenotype distributions, and transformations --- ## [HWE cutoffs for Rare variant analysis](https://isgw-forum.colorado.edu/t/hwe-cutoffs-for-rare-variant-analysis/775)
**Author:** [@budhbhatti.urvi.6921](https://isgw-forum.colorado.edu/u/budhbhatti.urvi.6921)\ **Replies:** 2\ **Last updated:** [June 4, 2026, 4:27am UTC](https://isgw-forum.colorado.edu/t/hwe-cutoffs-for-rare-variant-analysis/775 "2026-06-04T04:27:47Z")
Hii all This may be a very naive question but in standard GWAS QC, we usually remove variants that significantly deviate from Hardy-Weinberg equilibrium. However, for rare variant analyses like in SAIGE, HWE tests may b… --- ## [Are there good example publications on gwas conducted separately (controlling) for low vs high socioeconomic status families](https://isgw-forum.colorado.edu/t/are-there-good-example-publications-on-gwas-conducted-separately-controlling-for-low-vs-high-socioeconomic-status-families/783)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 5\ **Last updated:** [June 3, 2026, 11:14pm UTC](https://isgw-forum.colorado.edu/t/are-there-good-example-publications-on-gwas-conducted-separately-controlling-for-low-vs-high-socioeconomic-status-families/783 "2026-06-03T23:14:10Z")
Relatedly, are there good example publications on gwas conducted separately (controlling) for low vs high socioeconomic status families, like parental education (i dont mean within family gwas). I was always wondering wh… --- ## [What are the strengths and disadvantage of conducting GWAS that includes related individuals?](https://isgw-forum.colorado.edu/t/what-are-the-strengths-and-disadvantage-of-conducting-gwas-that-includes-related-individuals/781)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 11\ **Last updated:** [June 3, 2026, 7:59pm UTC](https://isgw-forum.colorado.edu/t/what-are-the-strengths-and-disadvantage-of-conducting-gwas-that-includes-related-individuals/781 "2026-06-03T19:59:59Z")
GWAS has been done with family-based samples (e.g., data from the Collaborative Study on the Genetics of Alcoholism \[COGA\] study). What are the strengths and disadvantage of conducting GWAS that includes related individu… --- ## [Typically what proportion of SNPs don't pass QC?](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 2\ **Last updated:** [June 3, 2026, 7:58pm UTC](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782 "2026-06-03T19:58:26Z")
typically what proportion of SNPs don’t pass QC? --- ## [Why should binary data have a 1:1 case:control ratio?](https://isgw-forum.colorado.edu/t/why-should-binary-data-have-a-1-1-case-control-ratio/780)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 3\ **Last updated:** [June 3, 2026, 7:55pm UTC](https://isgw-forum.colorado.edu/t/why-should-binary-data-have-a-1-1-case-control-ratio/780 "2026-06-03T19:55:39Z")
Why should binary data have a 1:1 case:control ratio? my understanding is that you can get more power/accuracy with a 1:4 case: control ratio for less common diseases? --- ## [Is the \*.ped the bed genotype matrix file?](https://isgw-forum.colorado.edu/t/is-the-ped-the-bed-genotype-matrix-file/779)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 2\ **Last updated:** [June 3, 2026, 7:54pm UTC](https://isgw-forum.colorado.edu/t/is-the-ped-the-bed-genotype-matrix-file/779 "2026-06-03T19:54:34Z")
is the \*.ped the bed genotype matrix file? --- ## [Is there a lift over package we can use from hg37 to hg38?](https://isgw-forum.colorado.edu/t/is-there-a-lift-over-package-we-can-use-from-hg37-to-hg38/769)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 4\ **Last updated:** [June 3, 2026, 2:24pm UTC](https://isgw-forum.colorado.edu/t/is-there-a-lift-over-package-we-can-use-from-hg37-to-hg38/769 "2026-06-03T14:24:43Z")
is there a lift over package we can use from hg37 to hg38 ? --- ## [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 --- ## [What is the typical rate of sex mismatches found during genetic QC](https://isgw-forum.colorado.edu/t/what-is-the-typical-rate-of-sex-mismatches-found-during-genetic-qc/770)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 4\ **Last updated:** [June 2, 2026, 11:14pm UTC](https://isgw-forum.colorado.edu/t/what-is-the-typical-rate-of-sex-mismatches-found-during-genetic-qc/770 "2026-06-02T23:14:44Z")
What is the typical rate of sex mismatches found during genetic QC? I’d like to know what is considered normal and what might be unusually high. --- ## [Which one is a more reliable genome build to use: hg37 or hg38?](https://isgw-forum.colorado.edu/t/which-one-is-a-more-reliable-genome-build-to-use-hg37-or-hg38/768)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 5\ **Last updated:** [June 2, 2026, 11:11pm UTC](https://isgw-forum.colorado.edu/t/which-one-is-a-more-reliable-genome-build-to-use-hg37-or-hg38/768 "2026-06-02T23:11:40Z")
Which one is a more reliable genome build to use: hg37 or hg38? --- ## [Is it better to have different cutoffs for HWE filtering](https://isgw-forum.colorado.edu/t/is-it-better-to-have-different-cutoffs-for-hwe-filtering/766)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 7\ **Last updated:** [June 2, 2026, 11:06pm UTC](https://isgw-forum.colorado.edu/t/is-it-better-to-have-different-cutoffs-for-hwe-filtering/766 "2026-06-02T23:06:25Z")
Is it better to have different cutoffs for HWE filtering based on sample size (considering working with different cohorts)? And if so, how should we set these cut offs? --- ## [Do the covariates included in a GWAS vary across different traits](https://isgw-forum.colorado.edu/t/do-the-covariates-included-in-a-gwas-vary-across-different-traits/765)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 2\ **Last updated:** [June 2, 2026, 11:04pm UTC](https://isgw-forum.colorado.edu/t/do-the-covariates-included-in-a-gwas-vary-across-different-traits/765 "2026-06-02T23:04:30Z")
Do the covariates included in a GWAS vary across different traits? How should we determine the most appropriate covariates for a GWAS analysis? --- ## [What is the downside of adding too many covariates?](https://isgw-forum.colorado.edu/t/what-is-the-downside-of-adding-too-many-covariates/764)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 1\ **Last updated:** [June 2, 2026, 10:59pm UTC](https://isgw-forum.colorado.edu/t/what-is-the-downside-of-adding-too-many-covariates/764 "2026-06-02T22:59:42Z")
What is the downside of adding too many covariates? Such as PC1-20 instead of just PC1-10, or including age2 and age, instead of just age, etc. --- ## [Practical links](https://isgw-forum.colorado.edu/t/practical-links/751)
**Author:** [@Elizabeth\_Prom-Worml](https://isgw-forum.colorado.edu/u/Elizabeth_Prom-Worml)\ **Replies:** 0\ **Last updated:** [June 1, 2026, 8:00pm UTC](https://isgw-forum.colorado.edu/t/practical-links/751 "2026-06-01T20:00:33Z")
Welcome to Day 2! Pre-lecture materials can be found here: Working with data | Institute for Behavioral Genetics | University of Colorado Boulder Please visit this link for our tutorial for the day. https://qimr.az1.qua…