<b>Motivation</b>: Large genomic datasets combining genotype and sequence data, such as for expression quantitative trait loci (eQTL) detection, require perfect matching between both data types.<br><b>Results</b>: We described here MBV (Match BAM to VCF); a method to quickly solve sample mislabeling and detect cross-sample contamination and PCR amplification bias.<br><b>Availability and Implementation</b>: MBV is implemented in C ++ as an independent component of the QTLtools software package, the binary and source codes are freely available at https://qtltools.github.io/qtltools/ .<br><b>Contact</b>: olivier.delaneau@unige.ch or emmanouil.dermitzakis@unige.ch.<br><b>Supplementary information</b>: Supplementary data are available at Bioinformatics online.<br>