jdalapicolla / BAG_SNPs

Script for estimating sample size for a germplasm/seeds bank (BAG) using allele frequency and genetic diversity of wild species/population based on SNPs

Allele Frequency and Genetic Diversity in seed/germoplasm bank using SNPs and resampled datasets

Script for estimating influence of sample size in a germplasm/seeds bank (BAG) using allele frequency and genetic diversity of a wild species/population

Ipomoaea in three steps:

1. Calculate Allele Frequency in a wild Species/Population using VCF

2. Calculate Allele Frequency in Resampled Datasets using a wild species/population as model using VCF.

3. Calculate Genetic Diversity in Resampled Datasets using a wild species/population as model using GENIND.

Pilocarupus in five steps:

1. Calculate Allele Frequency using GENIND objects (Null Alleles and Alleles > 50 copies) in natural populations and resampled populations with different sample size.

2. Calculate Genetic Diversity (HE) using GENIND objects in natural populations and resampled populations with different sample size.

3. Calculate Allele Richness (AR) using GENIND objects in natural populations and resampled populations with different sample size.

4. Calculate Nucleotide Diversity (PI) using VCF in natural populations and resampled populations with different sample size.

5. Calculate Effective Population Sizes (Ne) using GENIND objects in natural populations and resampled populations with different sample size.