Abstract: Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies CpG-SNP contamination markers. The CpG-SNP contamination markers include at least one SNP that affects a CpG site. The CpG-SNP contamination markers may include additive CpG-SNP sites and/or subtractive CpG-SNP sites. Additive CpG-SNP sites include an SNP that creates a new CpG site. Subtractive CpG-SNP sites include an SNP that removes a preexisting CpG site. Hybrid sites may include additional sites. A multiple CpG-SNP contamination marker comprises two or more CpG-SNP sites. A CpG-SNP & indel contamination marker comprises at least one CpG-SNP site and an indel site. For a given sample, the system identifies contamination markers for which the sample is homozygous. The system determines fragments having a haplotype that is different from the homozygous haplotype of the sample to be contamination fragments.