@article{bedtools,
  title    = "{BEDTools}: a flexible suite of utilities for comparing genomic
              features",
  author   = "Quinlan, Aaron R and Hall, Ira M",
  abstract = "MOTIVATION: Testing for correlations between different sets of
              genomic features is a fundamental task in genomics research.
              However, searching for overlaps between features with existing
              web-based methods is complicated by the massive datasets that are
              routinely produced with current sequencing technologies. Fast and
              flexible tools are therefore required to ask complex questions of
              these data in an efficient manner. RESULTS: This article
              introduces a new software suite for the comparison, manipulation
              and annotation of genomic features in Browser Extensible Data
              (BED) and General Feature Format (GFF) format. BEDTools also
              supports the comparison of sequence alignments in BAM format to
              both BED and GFF features. The tools are extremely efficient and
              allow the user to compare large datasets (e.g. next-generation
              sequencing data) with both public and custom genome annotation
              tracks. BEDTools can be combined with one another as well as with
              standard UNIX commands, thus facilitating routine genomics tasks
              as well as pipelines that can quickly answer intricate questions
              of large genomic datasets. AVAILABILITY AND IMPLEMENTATION:
              BEDTools was written in C++. Source code and a comprehensive user
              manual are freely available at http://code.google.com/p/bedtools
              CONTACT: aaronquinlan@gmail.com; imh4y@virginia.edu SUPPLEMENTARY
              INFORMATION: Supplementary data are available at Bioinformatics
              online.",
  journal  = "Bioinformatics",
  volume   =  26,
  number   =  6,
  pages    = "841--842",
  month    =  mar,
  year     =  2010,
  language = "en",
  doi      = {10.1093/bioinformatics/btq033}
}

@article {mosdepth,
  Title = {Mosdepth: quick coverage calculation for genomes and exomes},
  Author = {Pedersen, Brent S and Quinlan, Aaron R},
  DOI = {10.1093/bioinformatics/btx699},
  Number = {5},
  Volume = {34},
  Month = {March},
  Year = {2018},
  Journal = {Bioinformatics (Oxford, England)},
  ISSN = {1367-4803},
  Pages = {867—868},
  URL = {http://europepmc.org/articles/PMC6030888},
}

@article {coverage,
  Title = {Sequencing depth and coverage: key considerations in genomic analyses},
  Author = {Sims, David and Sudbery, Ian and Ilott, Nicholas E and Heger, Andreas and Ponting, Chris P},
  DOI = {10.1038/nrg3642},
  Number = {2},
  Volume = {15},
  Month = {February},
  Year = {2014},
  Journal = {Nature reviews. Genetics},
  ISSN = {1471-0056},
  Pages = {121—132},
  URL = {https://doi.org/10.1038/nrg3642},
}

@article {samformat,
  Title = {The Sequence Alignment/Map format and SAMtools},
  Author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and {1000 Genome Project Data Processing Subgroup}},
  DOI = {10.1093/bioinformatics/btp352},
  Number = {16},
  Volume = {25},
  Month = {August},
  Year = {2009},
  Journal = {Bioinformatics (Oxford, England)},
  ISSN = {1367-4803},
  Pages = {2078—2079},
  URL = {http://europepmc.org/articles/PMC2723002},
}
@article {bamtools,
	Title = {BamTools: a C++ API and toolkit for analyzing and managing BAM files},
	Author = {Barnett, Derek W and Garrison, Erik K and Quinlan, Aaron R and Strömberg, Michael P and Marth, Gabor T},
	DOI = {10.1093/bioinformatics/btr174},
	Number = {12},
	Volume = {27},
	Month = {June},
	Year = {2011},
	Journal = {Bioinformatics (Oxford, England)},
	ISSN = {1367-4803},
	Pages = {1691—1692},
	URL = {http://europepmc.org/articles/PMC3106182},
}

@article {poloni,
	Title = {A targeted next-generation gene panel reveals a novel heterozygous nonsense variant in the TP63 gene in patients with arrhythmogenic cardiomyopathy},
	Author = {Poloni, Giulia and Calore, Martina and Rigato, Ilaria and Marras, Elena and Minervini, Giovanni and Mazzotti, Elisa and Lorenzon, Alessandra and Li Mura, Ilena Egle Astrid and Telatin, Andrea and Zara, Ivano and Simionati, Barbara and Perazzolo Marra, Martina and Ponti, Jessica and Occhi, Gianluca and Vitiello, Libero and Daliento, Luciano and Thiene, Gaetano and Basso, Cristina and Corrado, Domenico and Tosatto, Silvio and Bauce, Barbara and Rampazzo, Alessandra and De Bortoli, Marzia},
	DOI = {10.1016/j.hrthm.2018.11.015},
	Number = {5},
	Volume = {16},
	Month = {May},
	Year = {2019},
	Journal = {Heart rhythm},
	ISSN = {1547-5271},
	Pages = {773—780},
	URL = {https://doi.org/10.1016/j.hrthm.2018.11.015},
}
@misc{phylosophy,
   author = "{Wikipedia contributors}",
   title = "Unix philosophy --- {W}ikipedia{,} The Free Encyclopedia",
   year = "2019",
   url = "https://en.wikipedia.org/w/index.php?title=Unix_philosophy&oldid=919880773",
   note = "[Online; accessed 20 December 2019 ]"
}

@misc{opt,
  author = {Weißl, Johannes},
  title = {cpp-optparse},
  year = {2017},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/weisslj/cpp-optparse}},
  commit = {2ec0b7aca9a692ff93017ed44ca9d13a8e7d4d00}
}

@dataset{dataset,
  author       = {Birolo, Giovanni and
                  Telatin, Andrea},
  title        = {{covtobed test files - 2 BAM files produced by 
                   target enrichment experiments}},
  month        = feb,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3643386},
  url          = {https://doi.org/10.5281/zenodo.3643386}
}
