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CAST-genomics / haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
https://haptools.readthedocs.io
MIT License
18 stars 4 forks source link

feat: `.snplist` input to `simphenotype` #217

Closed aryarm closed 1 year ago

aryarm commented 1 year ago

Instead of .hap files, users will be able to provide GCTA .snplist files! Refer to the docs for more info:

https://haptools--217.org.readthedocs.build/en/217/commands/simphenotype.html#examples

At the moment, we only recommend using .snplist files for SNPs -- although they may also work for repeats and haplotypes.

I'm not endorsing the use of .snplist files for other variants because we will probably need to deprecate that eventually. The issue is that .snplist files don't allow us to specify the type of effect (ex: repeat, haplotype, etc). Allowing users to specify any type of effect in their .snplist files may hinder efforts to add new types of effects in the future. The .hap format is designed to be flexible enough to allow us to expand the functionality of simphenotype without running into those issues.

aryarm commented 1 year ago

@gymreklab, is this along the lines of what you were looking for?

gymreklab commented 1 year ago

yes this sounds great! it will be a helpful convenience feature for SNP-only applications