svdetect_bam_preprocessing_pairs

svdetect_bam_preprocessing_pairs extracts abnormal read pairs from BAM files to support detection and classification of genomic structural variations from paired-end and mate-pair next-generation sequencing data.

Key Features:

• BAM preprocessing: Extracts anomalously mapped read pairs from BAM files produced by short-read aligners.
• Detection of structural variations: Leverages anomalous paired mappings to pinpoint large insertions-deletions, inversions, duplications, and balanced and unbalanced inter-chromosomal translocations.
• Analytical methods: Applies sliding-window and clustering strategies to analyze distributions of abnormal read pairs.
• Sequencing platform support: Processes data from platforms such as Illumina GA and ABI SOLiD.
• Output formats: Produces predicted structural variants in multiple file formats suitable for graphical visualization.

Scientific Applications:

• Genomic research: Enables identification and classification of structural variations to support studies of genetic disorders and genome evolution.
• High-throughput data analysis: Addresses computational processing of large paired-end and mate-pair next-generation sequencing datasets for downstream structural variant analysis.

Methodology:

Extracts anomalously mapped read pairs from BAM files generated by short-read aligners, applies sliding-window and clustering strategies to identify clusters of abnormal pairs, and outputs predicted structural variants in multiple file formats.