MTAG for other species

[heebokp]

Hello, thank you very much for the development and maintenance of the MTAG program.
Recently, I have engaged in conducting multitrait GWAS on the pig genome using the MTAG. During the MTAG program implementation, I encountered an issue with the number of chromosomes. The pig genome has a different number of chromosomes than expected by the MTAG. While pigs have 18 autosomes, the MTAG requires data up to 22 autosomes since it is based on the human genome. So, is there any solution to figure out the issues on the number of chromosomes?

[paturley]

Hello, We were not nearly creative enough in thinking through areas where MTAG would be applied, so we ended up hard coding the number of chromosomes in the software. If you can send us a log file that shows the error you are getting, then it will help us figure out the best way to help.

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On Tue, Jun 24, 2025 at 7:30 AM heebokp ***@***.***> wrote: *heebokp* created an issue (JonJala/mtag#237) <#237> Hello, thank you very much for the development and maintenance of the MTAG program. Recently, I have engaged in conducting multitrait GWAS on the pig genome using the MTAG. During the MTAG program implementation, I encountered an issue with the number of chromosomes. The pig genome has a different number of chromosomes than expected by the MTAG. While pigs have 18 autosomes, the MTAG requires data up to 22 autosomes since it is based on the human genome. So, is there any solution to figure out the issues on the number of chromosomes? — Reply to this email directly, view it on GitHub <#237>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5MZYEDGPKZOQMSKRG33FEZEXAVCNFSM6AAAAACAAAVECGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGE3TCNRSGY3TOOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[heebokp]

Thank you so much for the prompt response. Please find the attached file with error messages and more.

ldsc_mtag_pig.pdf

[JonJala]

It looks like you're running into issues in the sumstats.py file. If you make changes here and here , changing the 22 to 18, that might help unstick you? It's possible there are other areas of the code that have an assumption of 22 chromosomes, but this would be a good start.

[heebokp]

Thanks to your precise guidance, we were able to resolve the MTAG issue for pigs. We deeply appreciate your kind help!!