Evolutionary genomics based on PacBio HiFi long-read sequencing data reveals the importance of structural variants in shaping population-specific differences between Chinese and Indian rhesus macaques (Macaca mulatta)

Set-up: Make the Python scripts executable and compile the C++ programs

chmod u+x count_genotypes_ver_4.py
chmod u+x count_genotypes_ver_5.py
chmod u+x find_private_sv_ver_2.py
g++ -o bonferroni_vaf_bin_ver_2 bonferroni_vaf_bin_ver_2.cpp -lm
g++ -o find_significant_private_sv_ver_2 find_significant_private_sv_ver_2.cpp

Calculate population-specific allele frequencies

1. Prepare a tab-delimited .txt from the .vcf that contains basic information of each SVs (including chromosome, position, ID, SV type, SV length, and the genotype of each individual at the site)

   bcftools query -H -f '%CHROM\t%POS\t%ID\t%SVTYPE\t%SVLEN[\t%GT]\n' rhesus.SVs.vcf.gz -o rhesus.SVs.txt
   

   and then separate by population

   sed 's/#//' rhesus.SVs.txt | cut -f 1-15 > rhesus.SVs.Chi.txt
   sed 's/#//' rhesus.SVs.txt | cut -f 1-5,16- > rhesus.SVs.Ind.txt
   

2. Calculate the reference, alternative, and minor allele frequencies in both populations

   python3 ./count_genotypes_ver_4.py rhesus.SVs.Chi.txt rhesus.SVs.Chi.AF.txt
   python3 ./count_genotypes_ver_4.py rhesus.SVs.Ind.txt rhesus.SVs.Ind.AF.txt
   

Identify significant population-private SVs

1. Calculate the alternative allele count and frequency of each SV in each population

   python3 count_genotypes_ver_5.py rhesus.SVs.Chi.txt rhesus.SVs.Chi.AC.AF.txt
   python3 count_genotypes_ver_5.py rhesus.SVs.Ind.txt rhesus.SVs.Ind.AC.AF.txt
   

2. Merge the population-specific alternative allele counts and frequencies of each SV and add header information

   paste <(cut -f 1-8 rhesus.SVs.Chi.AC.AF.txt) <(cut -f 6-8 rhesus.SVs.Ind.AC.AF.txt) | sed '1d' > rhesus.SVs.AC.AF.txt
   { printf 'CHROM\tPOS\tID\tSVTYPE\tSVLEN\tChi_GENOS\tChi_VAC\tChi_VAF\tInd_GENOS\tInd_VAC\tInd_VAF\n'; cat rhesus.SVs.AC.AF.txt; } > tmp && mv tmp rhesus.SVs.AC.AF.txt
   

3. Identify population-private SVs

   python3 find_private_sv_ver_2.py rhesus.SVs.AC.AF.txt rhesus.SVs.PopPriv.txt
   sed '1d' rhesus.SVs.PopPriv.txt | awk '{if ($6 == "Chi") print}' > rhesus.SVs.PopPriv.Chi.txt
   sed '1d' rhesus.SVs.PopPriv.txt | awk '{if ($6 == "Ind") print}' > rhesus.SVs.PopPriv.Ind.txt
   

4. Apply a Bonferroni correction

   ./bonferroni_vaf_bin_ver_2 -in rhesus.SVs.PopPriv.Chi.txt -out rhesus.SVs.PopPriv.Chi.Bonferroni.txt
   ./bonferroni_vaf_bin_ver_2 -in rhesus.SVs.PopPriv.Ind.txt -out rhesus.SVs.PopPriv.Ind.Bonferroni.txt
   

5. Identify significant population-private SVs

   ./find_significant_private_sv_ver_2 -in rhesus.SVs.PopPriv.Chi.txt -cv rhesus.SVs.PopPriv.Chi.Bonferroni.txt -out rhesus.SVs.PopPriv.Chi.Bonferroni.signifiant.txt
   ./find_significant_private_sv_ver_2 -in rhesus.SVs.PopPriv.Ind.txt -cv rhesus.SVs.PopPriv.Ind.Bonferroni.txt -out rhesus.SVs.PopPriv.Ind.Bonferroni.signifiant.txt