How to calculate the allele frequency spectrum of a mixed ploidy population from a VCF file?

[Song-10-YF]

If I am calculating the allele frequency spectrum for a mixed ploidy group from a called VCF file, how should I set the parameters?

[isaacovercast]

Mixed ploidy like haploid and diploid? I'm not sure how the best way to do this is as I've never encountered this before. In practice if you set ploidy=1 or ploidy=2 with mixed haploid/diploid samples the results will be the same, but I would have to think more about how meaningful it would be. For polyploid samples set ploidy to the max ploidy value among all samples.

[Song-10-YF]

I have diploid and tetraploid in my vcf, so I should set it to 4? ------------------ Original ------------------ From: Isaac Overcast ***@***.***> Date: Fri,Dec 27,2024 11:46 PM To: isaacovercast/easySFS ***@***.***> Cc: Yan-Feng Song ***@***.***>, Author ***@***.***> Subject: Re: [isaacovercast/easySFS] How to calculate the allele frequencyspectrum of a mixed ploidy population from a VCF file? (Issue #70) Mixed ploidy like haploid and diploid? I'm not sure how the best way to do this is as I've never encountered this before. In practice if you set ploidy=1 or ploidy=2 with mixed haploid/diploid samples the results will be the same, but I would have to think more about how meaningful it would be. For polyploid samples set ploidy to the max ploidy value among all samples. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[isaacovercast]

Yes. Let me know how it goes, I have never tried this so I am curious.

[Song-10-YF]

I'll try it. But I'm not sure it's right either.

…

------------------ Original ------------------ From: Isaac Overcast ***@***.***> Date: Fri,Dec 27,2024 11:53 PM To: isaacovercast/easySFS ***@***.***> Cc: Yan-Feng Song ***@***.***>, Author ***@***.***> Subject: Re: [isaacovercast/easySFS] How to calculate the allele frequencyspectrum of a mixed ploidy population from a VCF file? (Issue #70) Yes. Let me know how it goes, I have never tried this so I am curious. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>