Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing"

Dataset type: Software
Data released on September 13, 2017

Pedersen BS; Collins RL; Talkowski ME; Quinlan AR (2017): Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing" GigaScience Database.


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: under the MIT license.

Additional details

Read the peer-reviewed publication(s):

Pedersen, B. S., Collins, R. L., Talkowski, M. E., & Quinlan, A. R. (2017). Indexcov: fast coverage quality control for whole-genome sequencing. GigaScience, 6(11), 1–6. doi:10.1093/gigascience/gix090

Additional information:

File NameSample IDData TypeFile FormatSizeRelease Date 
HTMLzip2.11 MB2017-08-25
Githubarchive4.79 MB2017-08-25
ReadmeTEXT1.46 KB2017-08-25
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Funding body Awardee Award ID Comments
National Institutes of Health R01HG006693
National Institutes of Health U24CA209999
Date Action
September 13, 2017 Dataset publish
October 17, 2017 Manuscript Link added : 10.1093/gigascience/gix090