SamJavascript

SamJavascript filters BAM files using JavaScript to enable custom, scriptable read-level selection for downstream genomic analyses such as variant calling and expression analysis.

Key Features:

• JavaScript-based filtering: Uses JavaScript expressions to define custom predicates for including or excluding reads in BAM (Binary Alignment/Map) files.
• Read-level criteria: Supports filtering by genomic regions, quality scores, and alignment metrics.
• Jvarkit integration: Distributes as part of the Jvarkit suite for compatibility with other Jvarkit utilities.

Scientific Applications:

• Read curation for variant calling: Generates filtered BAM subsets to improve accuracy of variant calling workflows.
• Expression analysis preprocessing: Selects reads for transcriptomic analyses such as expression quantification.
• Custom data stratification: Implements complex logical operations to create curated datasets based on alignment and metadata criteria.

Methodology:

Applies user-supplied JavaScript predicates to BAM records to include or exclude reads based on genomic coordinates, quality scores, and alignment metrics.