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Updated: Feb 20, 2026

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

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

Brent S Pedersen^1,2, Ryan L Collins^3,4,5, Michael E Talkowski^3,6,4,5

¹Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA.

|October 20, 2017

Summary

Indexcov efficiently estimates whole-genome sequencing coverage using BAM/CRAM linear indexes. This tool rapidly identifies aberrant coverage, chromosomal anomalies, batch effects, and sample sex, improving genomic data analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

BAM and CRAM file formats offer supplementary linear indexes for quick access to sequence alignment data.
These indexes enable inference of alignment records per genomic region, serving as a proxy for sequence depth.

Purpose of the Study:

To develop an efficient tool, indexcov, for estimating whole-genome sequencing coverage.
To enable rapid identification of samples with unusual coverage patterns, large-scale chromosomal anomalies, and potential batch effects.
To facilitate inference of sample sex based on coverage profiles.

Main Methods:

Utilizing the properties of BAM/CRAM linear indexes.
Comparing consecutive index entries to estimate alignment records per genomic region.
Developing the indexcov tool for efficient coverage estimation.

Main Results:

Indexcov provides an efficient method for whole-genome sequencing coverage estimation.
The tool can rapidly identify aberrant coverage profiles.
Indexcov aids in detecting large-scale chromosomal anomalies, batch effects, and inferring sample sex.

Conclusions:

Indexcov is an effective tool for analyzing whole-genome sequencing coverage.
The tool leverages existing file format features for rapid and accurate analysis.
Indexcov has broad applications in genomic data quality control and analysis.