# Question about SNP-heritability and alleles in PLINK

**URL:** https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755
**Category:** Downstream analysis with genomic data
**Tags:** plink, gcta
**Created:** [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")
**Posts on this page:** 1
**Page:** 1

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### Author: ![Shal](https://isgw-forum.colorado.edu/letter_avatar_proxy/v4/letter/s/2bfe46/32.png) [@Shal](https://isgw-forum.colorado.edu/u/Shal)
#### Post date: [June 2, 2026, 10:55am UTC](https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755/1 "2026-06-02T10:55:34Z")

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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 unrelated individuals, or would you normally recommend another tool (e.g. GCTA/BOLT, etc.) for this step?

I also had a related question about alleles in PLINK. I know you did not cover PLINK in the session, but could you briefly explain (or point me to a resource on) how to obtain or define the REF/ALT alleles and the effect allele when working with PLINK genotype data (i.e. bed/bim/fam files)? Do the genotype company provide that information using a ref panel?

Thanks

Shalini