Folded Spectrum in python is not recognizing some of the individuals in my VCF file

[Morgan L. Lynn]

Hello, with a few of my species in my pairwise analyses no data comes out after putting the vcf file into a folded spectrum. When I change the amount of called alleles from 10 (the true value) to 8 ( a random value I inputed) the folded spectrum is visible but only accounts for 2, or 3 of the alleles. This occurs with two other species where if I adjust the amount of called alleles in my populations the folded spectrum appears to have data, but when I use true values the folded spectrums are devoid of anything. Please help, I have attached examples of the issues I am seeing. 

[Ryan Gutenkunst]

Hello Morgan,

This may occur if you often have missing data. For a site to enter the spectrum for 10 alleles, you must have at least 10 successfully called alleles at that site. Is it possible (for example, due to low coverage) that you often have missing calls?

Best,

Ryan

On Oct 29, 2024, at 11:19 AM, 'Morgan L. Lynn' via dadi-user <dadi...@googlegroups.com> wrote:

Hello, with a few of my species in my pairwise analyses no data comes out after putting the vcf file into a folded spectrum. When I change the amount of called alleles from 10 (the true value) to 8 ( a random value I inputed) the folded spectrum is visible but only accounts for 2, or 3 of the alleles. This occurs with two other species where if I adjust the amount of called alleles in my populations the folded spectrum appears to have data, but when I use true values the folded spectrums are devoid of anything. Please help, I have attached examples of the issues I am seeing. <dadi-issues-adjusted-alleles.png><dadi-problem-no-data.png>

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<dadi-problem-no-data.png><dadi-issues-adjusted-alleles.png>