variant-analysis

name	variant-analysis
description	Annotate VCF variants with their type (SNP, MNP, INS, DEL) based on REF and ALT allele lengths. Use when parsing VCF files and classifying variant types from sequence changes.

Variant Analysis: VCF Variant Type Annotation

Overview

Given a VCF file, annotate each variant with its type (SNP, MNP, INS, DEL) based on the length difference between REF and ALT alleles.

Variant Type Classification Rules

From the REF and ALT alleles:

• SNP: REF and ALT differ by exactly 1 base (single nucleotide substitution)
• MNP: REF and ALT differ by more than 1 base but same length (multiple nucleotide substitution)
• INS: ALT is longer than REF (insertion)
• DEL: ALT is shorter than REF (deletion)

VCF Parsing

def parse_vcf(filepath):
    """Parse VCF file and return list of variant records."""
    variants = []
    with open(filepath) as f:
        for line in f:
            if line.startswith("#"):
                continue  # Skip header
            fields = line.strip().split("\t")
            chrom = fields[0]
            pos = int(fields[1])
            ref = fields[3]
            alt = fields[4]
            variants.append((chrom, pos, ref, alt))
    return variants

Variant Type Detection

def classify_variant_type(ref, alt):
    """Classify variant as SNP, MNP, INS, or DEL."""
    ref_len = len(ref)
    alt_len = len(alt)
    len_diff = alt_len - ref_len

    if len_diff == 0:
        # Same length - SNP or MNP
        if ref_len == 1:
            return "SNP"
        else:
            return "MNP"
    elif len_diff > 0:
        return "INS"
    else:
        return "DEL"

Complete Script

def parse_vcf(filepath):
    variants = []
    with open(filepath) as f:
        for line in f:
            if line.startswith("#"):
                continue
            fields = line.strip().split("\t")
            chrom = fields[0]
            pos = int(fields[1])
            ref = fields[3]
            alt = fields[4]
            variants.append((chrom, pos, ref, alt))
    return variants

def classify_variant_type(ref, alt):
    ref_len = len(ref)
    alt_len = len(alt)
    len_diff = alt_len - ref_len

    if len_diff == 0:
        return "SNP" if ref_len == 1 else "MNP"
    elif len_diff > 0:
        return "INS"
    else:
        return "DEL"

# Parse VCF and annotate
variants = parse_vcf("/root/input.vcf")

with open("/root/output.txt", "w") as f:
    for chrom, pos, ref, alt in variants:
        vtype = classify_variant_type(ref, alt)
        f.write(f"{chrom}:{pos} {vtype} {ref}>{alt}\n")

Output Format

chr1:100 SNP A>G
chr2:200 INS T>TA
chr3:300 DEL ACG>AC

Format: CHR:POS TYPE REF>ALT

Key Reference

• Parse VCF: skip header lines starting with #
• Fields: CHROM (0), POS (1), REF (3), ALT (4)
• Length comparison: INS if alt_len > ref_len, DEL if alt_len < ref_len, SNP/MNP if equal
• SNP: single base substitution (ref and alt both length 1)
• MNP: multi-base substitution (ref and alt same length > 1)