variants.bcftoolsFilter

Liatir.variants.bcftoolsFilter() filters variants by expression with bcftools filter -i and writes a bgzipped VCF (-O z).

Signature

bcftoolsFilter(args: BcftoolsFilterArgs): Promise<BcftoolsFilterResult>

Arguments

type BcftoolsFilterArgs = {
  input: string;        // input VCF/BCF
  outputVcf: string;    // where to write the filtered VCF (bgzipped)
  expression?: string;  // filter expression for `-i` (default "QUAL>20")
  threads?: number;     // worker threads
};

Result

type BcftoolsFilterResult = {
  outputVcf: string;    // path to the filtered VCF
  expression: string;   // the expression that was applied
};

Example

const { outputVcf } = await Liatir.variants.bcftoolsFilter({
  input: "/path/to/variants.vcf.gz",
  outputVcf: "/path/to/filtered.vcf.gz",
  expression: "QUAL>30 && DP>10",
});

Throws if bcftools exits non-zero. Requires the bcftools binary — check availability with Liatir.deps.check.