To get population specific CONSENSUS VCF files the VCF file produced with 'bcftools call' was first re-coded into population specific VCF files with 'vcftools'. Further the population specific VCF file containing multiple individuals was parsed with 'vcfparser.py mvcf2consensus' to obtain a CONSENSUS VCF file for each population. This CONSENSUS VCF files were used to generate pseudo-genomes files per natural population with 'vcfparser.py vcf2fasta' using also the masking regions (see "Get masking regions for individual samples and natural populations").
vcftools example for the population _Mus musculus musculus AFG_:
### Calculate K80 distance between populations using the CONSENSUS pseudo-genome files
## Nucleotide diversity calculations
### Get individual specific SNPs
To get individual specific VCF files the VCF file produced with 'bcftools call' was first re-coded for each individual with 'vcftools'. Further the individual specific VCF files were used to generate pseudo-genomes files per individual with 'vcfparser.py vcf2fasta' using individual masking regions (see "Get masking regions for individual samples and natural populations").
vcftools example for individual 396 of the population _Mus musculus musculus AFG_:
```
#example for individual 396 of the population Mmm_AFG: