gdtools_intersect

gdtools_intersect generates a Genome Diff file containing only mutations present in all input Genome Diff files to identify shared variants across datasets produced by next-generation DNA sequencing.

Key Features:

• Galaxy integration: Operates within the Galaxy framework for execution and data provenance tracking.
• Intersection of Genome Diff files: Computes the intersection of genomic variants across multiple Genome Diff files to produce a new Genome Diff file of shared mutations.
• Support for large-scale datasets: Handles multiple input Genome Diff files from high-throughput next-generation DNA sequencing analyses.
• Reproducibility and provenance: Records computational analyses within Galaxy histories to enable reproducibility and transparent inspection of inputs and outputs.

Scientific Applications:

• Comparative genomics: Identifying shared mutations across genomes or strains to highlight conserved variants.
• Cancer research: Detecting common oncogenic or recurrent mutations across tumor samples or cohorts.
• Population genetics: Identifying mutations shared across samples or cohorts for studies of allele sharing and variant distribution.

Methodology:

Performs systematic comparison of input Genome Diff files to identify and compile mutations present in all inputs, executed within the Galaxy environment to capture provenance.