Results: We described here MBV (Match BAM to VCF); a method to quickly solve sample mislabeling and detect cross-sample contamination and PCR amplification bias.  ...  Motivation: Large genomic datasets combining genotype and sequence data, such as for expression quantitative trait loci (eQTL) detection, require perfect matching between both data types.  ...  This method can be applied to a single or a collection of samples to detect a variety of issues involving mismatches between sequences and genotypes such as sample mislabeling, cross-sample contaminations  ...