PT  - JOURNAL ARTICLE
AU  - Pedersen, Brent S.
AU  - Collins, Ryan L.
AU  - Talkowski, Michael E.
AU  - Quinlan, Aaron R.
TI  - Indexcov: fast coverage quality control for whole-genome sequencing
AID  - 10.1101/148296
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 148296
4099  - http://biorxiv.org/content/early/2017/06/09/148296.short
4100  - http://biorxiv.org/content/early/2017/06/09/148296.full
AB  - 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.