pindel2vcf

pindel2vcf converts Pindel output into VCF and indexes variant calls to enable analysis of indels and other structural variants detected from paired-end short-read sequencing data.

Key Features:

• Breakpoint detection (Pindel pattern growth): Uses Pindel's pattern growth approach to identify breakpoints of large deletions and medium-sized insertions from paired-end short reads.
• VCF conversion: Converts Pindel-format variant calls into Variant Call Format (VCF) for interoperability with downstream tools.
• Indexing: Produces indexed VCF outputs to facilitate efficient querying and analysis of variant data.
• Validation: Methodology has been validated on both simulated reads and real sequencing data, demonstrating high efficiency and accuracy in identifying structural variants.
• Computational integration: Compatible with Galaxy and runnable within Galaxy@Pasteur, including execution on the Institut Pasteur cluster.

Scientific Applications:

• Genomic research: Supports detection and cataloging of structural variants for studies of genetic diversity and genome structure.
• Clinical genomics: Enables identification of indels relevant to genetic diagnosis and interpretation in clinical sequencing.
• Metagenomic analysis: Applicable in metagenomic workflows (e.g., MetaGenSense) for detecting structural variation in complex microbial communities.

Methodology:

Pindel's pattern growth algorithm identifies breakpoints from paired-end short reads, and outputs are converted to VCF and indexed for downstream analysis.