Abstract The collection of immunoglobulin genes in an individual’s germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of the several hundred known V alleles. Furthermore, the currently-accepted set of known V alleles is both incomplete (particularly for non-European samples), and contains a significant number of spurious alleles. The resulting uncertainty as to which immunoglobulin alleles are present in any given sample results in inaccurate B cell receptor sequence annotations, and in particular inaccurate inferred naive ancestors. In this paper we first show that the currently widespread practice of aligning each sequence to its closest match in the full set of IMGT alleles results in a very large number of spurious alleles that are not in the sample’s true set of germline V alleles. We then describe a new method for inferring each individual’s germline gene set from deep sequencing data, and show that it improves upon existing methods by making a detailed comparison on a variety of simulated and real data samples. This new method has been integrated into the partis annotation and clonal family inference package, available at https://github.com/psathyrella/partis , and is run by default without affecting overall run time. Author Summary Antibodies are an important component of the adaptive immune system, which itself determines our response to both pathogens and vaccines. They are produced by B cells through somatic recombination of germline DNA, which results in a vast diversity of antigen binding affinities across the B cell repertoire. We typically learn about the development of this repertoire, and its history of interaction with antigens, by sequencing large numbers of the DNA sequences from which antibodies are derived. In order to understand such data, it is necessary to determine the combination of germline V, D, and J genes that was rearranged to form each such B cell receptor sequence. This is difficult, however, because the immunoglobulin locus exhibits an extraordinary level of diversity across individuals – encompassing both allelic variation and gene duplication, deletion, and conversion – and because the locus’s large size and repetitive structure make germline sequencing very difficult. In this paper we describe a new computational method that avoids this difficulty by inferring each individual’s set of immunoglobulin germline genes directly from expressed B cell receptor sequence data.