vcfx

VCFx comprises a series of tools to deal with VCF (variant call format) files.

You may create complete sequences in Fasta format (keeping phase information).
You can treat uncertain genotypes and refine variants.
You can convert the VCF file into different formats, including Arlequin, Genepop, Haploview, etc.

Current VCFx version: 2.0.6b

How to install:
Download the source and follow the instructions in the manual.
 
How to cite VCFx:
Castelli et al. HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples. Hum Immunol. 2015 Dec;76(12):945-53. doi: 10.1016/j.humimm.2015.06.016
Lima et al. HLA-F coding and regulatory segments variability determined by massively parallel sequencing procedures in a Brazilian population sample. Hum Immunol. 2016 Dec;76(10):841-853. doi: 10.1016/j.humimm.2016.07.231