public List<String> getNewHeaderLines() {
		ArrayList<String> newLines = new ArrayList<String>();

		newLines.add("##SnpEffVersion=\"" + version + "\"");
		newLines.add("##SnpEffCmd=\"" + commandLineStr + "\"");

		// Fields changed in different format versions
		if (formatVersion == FormatVersion.FORMAT_SNPEFF_2) newLines.add("##INFO=<ID=EFF,Number=.,Type=String,Description=\"Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon [ | ERRORS | WARNINGS ] )' \">");
		else if (formatVersion == FormatVersion.FORMAT_SNPEFF_3) newLines.add("##INFO=<ID=EFF,Number=.,Type=String,Description=\"Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon [ | ERRORS | WARNINGS ] )' \">");
        else if (formatVersion == FormatVersion.FORMAT_SNPEFF_CBMI)
            newLines.add("##INFO=<ID=EFF,Number=.,Type=String,Description=\"Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change |  Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Rank | Segment | HGVS_DNA_nomenclature | HGVS_protein_nomenclature [ | ERRORS | WARNINGS ])' \">");
        else
            newLines.add("##INFO=<ID=EFF,Number=.,Type=String,Description=\"Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype_Number [ | ERRORS | WARNINGS ] )' \">");

		if (lossOfFunction) {
			newLines.add("##INFO=<ID=LOF,Number=.,Type=String,Description=\"Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' \">");
			newLines.add("##INFO=<ID=NMD,Number=.,Type=String,Description=\"Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' \">");
		}

		if (useOicr) newLines.add("##INFO=<ID=OICR,Number=.,Type=String,Description=\"Format: ( Transcript | Distance from begining cDNA )\">");

		return newLines;
	}