ppBAM

ppBAM performs on-the-fly genotyping of thousands of sequencing reads using server-side Smith-Waterman alignment against reference and mutated sequences to identify genetic variants.

Key Features:

• Server-side computing: Uses server-side computing to enable efficient performance for large-scale read genotyping.
• Smith-Waterman genotyping: Performs on-the-fly genotyping of thousands of reads via Smith-Waterman alignment of sequencing data to reference and mutated sequences.
• ClustalO realignment: Realigns reads against a mutated reference sequence using ClustalO to improve visualization of support for complex variants.
• GDC BAM slicing API integration: Integrates with the National Cancer Institute Genomic Data Commons (GDC) BAM slicing API to access BAM slices from cancer sequencing datasets.
• Reinterpretation support: Facilitates examination and reinterpretation of variant calls through combined realignment and genotyping.

Scientific Applications:

• Cancer genomics: Supports analysis of intricate genomic alterations commonly encountered in cancer genomics.
• Variant interpretation: Enables identification and re-evaluation of genetic variants from sequencing reads by aligning against reference and mutated sequences.
• GDC dataset analysis: Allows examination of extensive cancer sequencing datasets accessed via the Genomic Data Commons BAM slicing API.

Methodology:

Computational steps include server-side processing, Smith-Waterman alignment for per-read genotyping, realignment of reads to a mutated reference using ClustalO, and retrieval of BAM slices via the GDC BAM slicing API.