VariantBam

VariantBam filters and profiles sequencing reads and read-pairs in BAM, CRAM, and SAM files to enable targeted extraction of variant-supporting and motif-matching reads for downstream genomic analyses.

Key Features:

• Flexible filtering framework: Extracts specific reads or read-pairs using customizable rules defined by genomic intervals or variant sites.
• Comprehensive filters: Applies filters that operate on alignment data, sequence motifs, regional coverage, and base quality.
• Efficient data management: Removes extraneous tags and selects high-quality variant-supporting and motif-matching reads, achieving a reported median size reduction ratio of 3.1:1 in an application on 10 lung cancer whole-genome BAM files.
• Implementation: Implemented in C++ to operate on large sequencing files (BAM, CRAM, SAM) efficiently.

Scientific Applications:

• Next-generation sequencing workflows: Enables targeted read selection and storage reduction within NGS datasets.
• Cancer genomics: Facilitates extraction of reads supporting somatic variants for tumor genome analysis.
• Personalized medicine: Supports selection of variant-supporting reads for individual genomic profiling.
• Genetic profiling and validation: Focuses downstream analyses on high-quality reads matching specific variants or sequence motifs.

Methodology:

Applies user-defined filters based on genomic intervals or variant sites to BAM, CRAM, and SAM files, operating on alignment data, sequence motifs, regional coverage, and base quality, and optionally removes extraneous tags to extract reads or read-pairs.