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Check a VCF header and detect its source (caller)

Source: R/vcf.R
check_header_source_vcf.Rd

Inspect the VCF header (via SeqArray::seqVCF_Header()) to:

  • fix known FORMAT/INFO inconsistencies (Stacks, samtools/freebayes-style),

  • detect the variant caller / pipeline (Stacks, freebayes, bcftools, GATK, etc.),

  • flag whether the VCF comes from Stacks,

  • suggest reasonable INFO/FORMAT subsets for import,

  • return a cleaned header object for safe import into GDS.

The function preserves the original ##source= line (if present) and returns it as vcf.source.raw. Classification into a standardised descriptor is returned as data.source.

Usage

check_header_source_vcf(vcf, markers.info = NULL, vcf.metadata = NULL)

Arguments

vcf

(character) Path to a VCF file (optionally bgzipped).

markers.info

(optional, character) Names of INFO fields to import. If NULL, caller-specific defaults are used when available; if those are also NULL, all INFO fields are imported. Any values not present in the header are silently dropped.

Default: markers.info = NULL.

vcf.metadata

(optional) Controls which FORMAT fields are imported:

  • NULL: use caller-specific defaults (if any), otherwise import all FORMAT fields;

  • logical: TRUE = import all FORMAT fields, FALSE = import only GT;

  • character: explicit list of FORMAT field IDs to import; GT is always added if missing. Any fields not present in the header are silently dropped.

Default: vcf.metadata = NULL.

Value

A list with:

  • data.source – inferred caller (e.g. "bcftools", "freebayes", …);

  • vcf.source.raw – exact raw ##source= string or NA;

  • stacks.check – whether this is a Stacks VCF (TRUE/FALSE);

  • check.header – cleaned SeqArray::seqVCF_Header() object;

  • markers.info – final INFO fields to import (or NULL = all);

  • overwrite.metadata – final FORMAT fields to import (or NULL = all).