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 also convert the VCF data in different formats, including Arlequin (.arp) and an input file to be used with the PHASE algorithm (.inp).

Current VCFx version: 1.2b

Whats's new on version 1.2b
- bug fixed: vcfx fasta was crashing when dealing with multi-line fasta reference

Download vcfx manual

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How to cite VCFx:
VCFx was introduced in two manuscripts. Please cite them both.
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


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Molecular Genetics and Bioinformatics Lab