变异检测与统计：参数与补充说明¶

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

计算满足注释与频率条件的编码变异比例¶

dnakit.databases.coding_variant_fraction(*, file, vaf_threshold=None, annotation=None, header_rows=None, vaf_col=None, so_col=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`file`	string	必填	Path to variant Excel (.xlsx) or CSV file.
`vaf_threshold`	number	None	Keep variants with VAF strictly less than this value. Default 0.3.
`annotation`	string	None	Sequence Ontology term to count in numerator. Default 'synonymous_variant'.
`header_rows`	integer	None	1 for flat headers, 2 for MultiIndex (common in Excel variant reports). Default 1.
`vaf_col`	string \| null	None	Explicit VAF column name. If empty, auto-detect from 'variant allele freq' or 'vaf'.
`so_col`	string \| null	None	Explicit Sequence Ontology column name. If empty, auto-detect from 'sequence ontology'.
`verbose`	bool	True	运行提示开关。

dnakit.databases.vcf_count_variants(*, operation=None, vcf_path, pass_only=None, regions=None, min_qual=None, include_expr=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	必填	Path to a local .vcf, .vcf.gz, or .bcf file
`pass_only`	boolean \| null	None	If true, count only FILTER=PASS or '.' records
`regions`	string \| null	None	Restrict to a region, e.g. 'chr1' or 'chr1:1-1000000'
`min_qual`	number \| null	None	Keep only records with QUAL >= this value
`include_expr`	string \| null	None	Extra bcftools -i include expression, e.g. 'INFO/AF>0.01'
`verbose`	bool	True	运行提示开关。

dnakit.databases.vcf_normalize(*, operation=None, vcf_path, multiallelics=None, reference_fasta=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	必填	Path to a local .vcf, .vcf.gz, or .bcf file
`multiallelics`	string \| null	None	'split' (default) breaks multiallelic records into biallelic; 'join' merges; 'none' leaves as-is
`reference_fasta`	string \| null	None	Optional reference FASTA path; enables indel left-alignment (-f)
`verbose`	bool	True	运行提示开关。

dnakit.databases.vcf_summary_stats(*, operation=None, vcf_path, pass_only=None, regions=None, min_qual=None, include_expr=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	必填	Path to a local .vcf, .vcf.gz, or .bcf file
`pass_only`	boolean \| null	None	If true, count only FILTER=PASS or '.' records
`regions`	string \| null	None	Restrict to a region, e.g. 'chr1' or 'chr1:1-1000000' (streamed, no index needed)
`min_qual`	number \| null	None	Keep only records with QUAL >= this value
`include_expr`	string \| null	None	Extra bcftools -i include expression, e.g. 'INFO/DP>10'
`verbose`	bool	True	运行提示开关。