New in v.0.1.4: haplo2fstat with Map-independent imputations using Random Forest

This new release introduce haplo2fstat function.
Similar to the other 'haplo2...' functions, you can choose to imputed the missing data with random forest or the most frequent allele.

New in v.0.1.3: Map-independent imputations of a VCF

This new release enable map-independent imputations of a VCF file created by STACKS. Two options are available for imputations: using Random Forest or the most frequent category.

Before imputations, the VCF file can be filtered with:

• a whitelist of loci (to keep only specific loci...)
• a blacklist of individuals (to remove individuals or entire populations...)

Also, a list of genotypes with bad coverage and/or genotype likelihood can be supplied to erase the genotypes before imputations (for more details look at the function: blacklist_erase_genotype).

Imputations: Random Forest and most frequent allele.

New release with imputations using Random Forest or the most frequent allele.
The imputations computations are included in 3 functions: haplo2genepop, haplo2genind and haplo2gtypes.

works with stacks v.1.32 and Alysse's data

Changed string script in read_stacks_vcf and filter_all

First release

Testing first release with Zenodo to track with DOI