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Per the snp_diversity.py script, documentation states: Only quantify diversity at synonymous sites (Note: use the ratio of 5/6 for pN/pS)
What does this mean? Is pN/pS calculated by running:
snp_diversity.py /path/to/snps --genomic_type per-gene --site_type 1D --locus_type CDS --out /path/to/output
Per the snp_diversity.py script, documentation states: Only quantify diversity at synonymous sites (Note: use the ratio of 5/6 for pN/pS)
What does this mean? Is pN/pS calculated by running:
snp_diversity.py /path/to/snps --genomic_type per-gene --site_type 1D --locus_type CDS --out /path/to/output
and then:
snp_diversity.py /path/to/snps --genomic_type per-gene --site_type 4D --locus_type CDS --out /path/to/output
And then taking the pi value in the output for 1D/pi value in the output for 4D?
What does the ratio of 5/6 have to do with it?
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