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Indexcov: fast coverage quality control for whole-genome sequencing

Brent S. Pedersen, Ryan L. Collins, Michael E. Talkowski, Aaron R. Quinlan
doi: https://doi.org/10.1101/148296
Brent S. Pedersen
1Department of Human Genetics, University of Utah, Salt Lake City, UT
3USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT
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Ryan L. Collins
4Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
6Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
7Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA.
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Michael E. Talkowski
4Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
5Department of Neurology, Harvard Medical School, Boston, MA
6Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
7Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA.
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Aaron R. Quinlan
1Department of Human Genetics, University of Utah, Salt Lake City, UT
2Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
3USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT
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Abstract

The BAM1 and CRAM2 formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at: https://github.com/brentp/goleft under the MIT license.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 09, 2017.
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Indexcov: fast coverage quality control for whole-genome sequencing
Brent S. Pedersen, Ryan L. Collins, Michael E. Talkowski, Aaron R. Quinlan
bioRxiv 148296; doi: https://doi.org/10.1101/148296
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Indexcov: fast coverage quality control for whole-genome sequencing
Brent S. Pedersen, Ryan L. Collins, Michael E. Talkowski, Aaron R. Quinlan
bioRxiv 148296; doi: https://doi.org/10.1101/148296

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