Antibody haplotype inference (chromosomal phasing) may have clinical implications for the identification of genetic predispositions to diseases. Yet, our knowledge of the genomic loci encoding for the variable regions of the antibody is only partial, mostly due to the challenge of aligning short reads from genome sequencing to these highly repetitive loci. A powerful approach to infer the content of these loci relies on analyzing repertoires of rearranged V(D)J sequences. We present here RAbHIT, an R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework. RAbHIT offers inference of haplotype and gene deletions. It may be applied to sequences from naïve and non-naïve B-cells, sequenced by different library preparation protocols.