Variant Calling and Statistics: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Calculate the fraction of coding variants matching filters¶

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

Parameter	Type	Required / default	Description and constraints
`file`	string	Required	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	Progress flag.

Count filtered variants in a VCF or BCF file¶

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

Parameter	Type	Required / default	Description and constraints
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	Required	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	Progress flag.

Normalize VCF variants and multiallelic sites¶

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

Parameter	Type	Required / default	Description and constraints
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	Required	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	Progress flag.

Summarize VCF variant types and sample genotype statistics¶

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

Parameter	Type	Required / default	Description and constraints
`operation`	object \| None	None	Operation (fixed)
`vcf_path`	string	Required	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	Progress flag.