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get Multi-Nucleotide Variants

get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences. MNVs occur when multiple Single Nucleotide Variants (SNVs) are present within the same codon, leading to the translation of a different amino acid. This tool addresses limitations in current annotation programs like ANNOVAR or SnpEff, which are primarily designed to work with individual SNVs and might overlook the actual amino acid changes resulting from MNVs.

get_MNV seeks to address this issue, enhancing the comprehensiveness of genetic variant interpretation.

IMPORTANT this script works with SNV against a reference, insertions and deletions modifiying reading frame are not currently supported

Features

• MNV Identification: Detects SNVs occurring within the same codon and reclassifies them as MNVs.
• Accurate Amino Acid Change Calculation: Computes the resulting amino acid changes based on genomic reads.
• Integration with BAM and VCF Files: Supports input from VCF files for variants and optional BAM files for aligned reads.
• Quality Analysis: Allows setting a minimum Phred quality threshold to filter out low-quality reads.