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PMID: 29048539 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Indexcov: fast coverage quality control for whole-genome sequencing.

GigaScience ·Vol. 6 ·No. 11 ·2017-00-01 ·Pages 1-6

Pedersen BS, Collins RL, Talkowski ME, Quinlan AR

Abstract

The BAM and CRAM 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.

MeSH Terms
Genome, Human Humans Quality Control Reproducibility of Results Sequence Alignment/methods,standards Software/standards Whole Genome Sequencing/methods,standards
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Pedersen Brent S
Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA. | USTAR Center for Genetic Discovery, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA.
Collins Ryan L
Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114, USA. | Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, 415 Main St, Cambridge, MA 02142, USA. | Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, A-111, 25 Shattuck St, Boston, MA 02115, USA.
Talkowski Michael E
Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114, USA. | Department of Neurology, Harvard Medical School, A-111, 25 Shattuck St, Boston, MA 02115, USA. | Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, 415 Main St, Cambridge, MA 02142, USA. | Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, A-111, 25 Shattuck St, Boston, MA 02115, USA.
Quinlan Aaron R
Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA. | Department of Biomedical Informatics, University of Utah, 421 Wakara Way #140, Salt Lake City, UT 84108, USA. | USTAR Center for Genetic Discovery, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA.
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Article Info
Journal
GigaScience
Abbr.
Gigascience
ISSN
2047-217X
DOI
10.1093/gigascience/gix090
Published
2017-00-01
Pages
1-6
Language
English
Region
United States
NLM ID
101596872
PMCID
PMC5737511
Subset
IM
Grants
NIGMS NIH HHS · R01 GM124355 · United States
NHGRI NIH HHS · R01 HG006693 · United States
NCI NIH HHS · U24 CA209999 · United States
External Links
PubMed source DOI: 10.1093/gigascience/gix090 PMC Full Text View journal details
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