Indexcov

Indexcov estimates sequencing coverage across whole genomes from BAM and CRAM files by analyzing their linear indexes to infer alignment record density as a proxy for sequence depth.

Key Features:

• Rapid Estimation: Provides coverage estimates in seconds per genome enabling efficient processing of large datasets.
• 16KB Resolution: Uses the 16KB resolution of BAM indexes to generate localized coverage estimates.
• Aberrant Coverage Identification: Identifies samples with aberrant coverage profiles for sequencing quality control.
• Chromosomal Anomaly Detection: Reveals large-scale chromosomal anomalies by analyzing genome-wide coverage patterns.
• Batch Effect Recognition: Detects potential batch effects across high-throughput sequencing experiments by comparing coverage patterns across samples.
• Sex Inference: Infers sample sex from coverage differences on sex chromosomes.

Scientific Applications:

• Sequencing Quality Control: Rapidly screens whole-genome sequencing samples for coverage anomalies and quality issues.
• Large-Scale Genomic Studies: Enables fast coverage assessment across cohorts in large-scale genomic studies.
• Chromosomal Anomaly Screening: Supports detection of large-scale chromosomal anomalies from coverage patterns.
• Batch Effect Detection: Identifies batch-related coverage differences to preserve data integrity across experiments.
• Sex Inference for Analyses: Provides sample sex inference for population genetics and personalized medicine studies.

Methodology:

Indexcov compares consecutive entries in the BAM or CRAM linear index (leveraging the 16KB resolution of BAM indexes) to infer the number of alignment records per genomic region as a proxy for sequence depth, enabling rapid coverage approximation without reading full alignments.