Update snp_diversity.md

Author: snayfach

docs/snp_diversity.md

@@ -72,18 +72,21 @@ Site filters (select subset of genomic sites from INDIR):
 2) Quantify between-sample heterogenity genome-wide  
 `snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type pooled-sample --out /path/to/output`
 
-3) Quantify between-sample heterogenity per-gene 
+3) Quantify between-sample heterogenity per-gene  
 `snp_diversity.py /path/to/snps --genomic_type per-gene --sample_type pooled-samples --out /path/to/output`
 
 4) Use downsampling to control the read-depth at each genomic site  
 `snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type per-sample --out /path/to/output`
 
 5) Only quantify diversity at non-synonymous sites  
+`snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type pooled-samples --site_type 1D --locus_type CDS --out /path/to/output`
+
+6) Only quantify diversity at synonymous sites (Note: use the ratio of 5/6 for pN/pS)   
 `snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type pooled-samples --site_type 4D --locus_type CDS --out /path/to/output`
 
-6) Quantify SNPs using a different definition of a polymorphism  
+7) Quantify SNPs using a different definition of a polymorphism  
 `snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type per-sample --snp_maf 0.05 --out /path/to/output`
 
-7) Run a quick test  
+8) Run a quick test  
 `snp_diversity.py /path/to/snps --max_sites 10000  --out /path/to/output`