Virmid

Virmid performs virtual microdissection to call single nucleotide polymorphisms (SNPs) in disease-control matched samples by modeling sample contamination (alpha) to enable detection of low-allele-frequency variants.

Key Features:

• Virtual microdissection: Performs virtual microdissection to deconvolute mixed or contaminated samples for variant analysis.
• Contamination handling: Models and accounts for contamination within individual samples using a contamination parameter (alpha).
• Low-allele-frequency SNP detection: Enables discovery of SNPs at low allele frequency by incorporating contamination level into variant calling.
• Disease-control matched analysis: Tailored for analyses of matched disease and control samples to identify disease-associated genetic variation.

Scientific Applications:

• Impure or heterogeneous sample analysis: SNP calling in studies where sample purity cannot be guaranteed, such as contaminated clinical or mixed-cell samples.
• Disease genetics: Identification of genetic variations associated with disease in disease-control matched cohorts to support studies of disease etiology and downstream translational research.

Methodology:

Models contamination using an alpha parameter and applies virtual microdissection to perform SNP calling in disease-control matched samples.