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3_calculate_pop_gen_stats.txt
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3_calculate_pop_gen_stats.txt
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################################################################################################
#
# 3. Calculating population genetic statistics
#
#
################################################################################################
# Calculate FST between populations using vcftools
# Need to calculate FST between all possible pairs (3 combinations)
# gloria_samples.txt contains a list of sample IDs for gloria individuals
# banos_samples.txt contains a list of sample IDs for banos individuals
# esperanza_samples.txt contains a list of sample IDs for esperanza individuals
vcftools --vcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --weir-fst-pop gloria_samples.txt --weir-fst-pop banos_samples.txt --out gloria_and_banos_fst
vcftools --vcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --weir-fst-pop gloria_samples.txt --weir-fst-pop esperanza_samples.txt --out gloria_and_esperanza_fst
vcftools --vcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --weir-fst-pop banos_samples.txt --weir-fst-pop esperanza_samples.txt --out banos_and_esperanza_fst
# Calculate Transition/Transversion ratio
vcftools --vcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --TsTv-summary --out transition_transversion_ratio
# Separate merged vcf file into separate files per population to calculate inbreeding coefficient
vcftools --gzvcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --keep gloria_samples.txt --recode --recode-INFO-all --out gloria_snps_minDP8_maxmiss0.9_minQ30_hwe0.05
vcftools --gzvcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --keep banos_samples.txt --recode --recode-INFO-all --out banos_snps_minDP8_maxmiss0.9_minQ30_hwe0.05
vcftools --gzvcf merged_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --keep esperanza_samples.txt --recode --recode-INFO-all --out esperanza_snps_minDP8_maxmiss0.9_minQ30_hwe0.05
# Calculate inbreeding coefficient for each population
vcftools --vcf gloria_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --het --out gloria_inbreeding
vcftools --vcf banos_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --het --out banos_inbreeding
vcftools --vcf esperanza_snps_minDP8_maxmiss0.9_minQ30_hwe0.05.recode.vcf --het --out esperanza_inbreeding