Alexandre Fort1, Nikolaos I Panousis1,2,3, Marco Garieri1,2,3, Stylianos E Antonarakis1,3, Tuuli Lappalainen4,5, Emmanouil T Dermitzakis1,2,3, Olivier Delaneau1,2,3. 1. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland. 2. Swiss Institute of Bioinformatics, Lausanne, Switzerland. 3. Institute of Genetics and Genomics in Geneva, Geneva, Switzerland. 4. New York Genome Center, New York, USA. 5. Department of Systems Biology, Columbia University, New York, USA.
Abstract
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. 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. AVAILABILITY AND IMPLEMENTATION: 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/ . CONTACT: olivier.delaneau@unige.ch or emmanouil.dermitzakis@unige.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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. 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. AVAILABILITY AND IMPLEMENTATION: 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/ . CONTACT: olivier.delaneau@unige.ch or emmanouil.dermitzakis@unige.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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