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Check a VCF for common variant-level problems and remove the offenders

Source: R/discarded_variants.R
check_and_remove_discarded_variants.Rd

Removes:

  • Rows with identical REF and ALT.

  • Stray #CHROM header repeats.

  • Duplicated (CHROM, POS, REF, ALT) rows (keeping one copy).

  • Multiple-ALT rows (comma-separated ALT field).

  • Non-standard chromosome names (or those outside chr_names_to_process when supplied).

  • Substitutions of length > 2 (e.g. ACT>TGA).

  • Complex indels (REF[1] != ALT[1]).

  • Wrong DBS rows where REF and ALT share a base at the same position.

  • Variants whose REF base is not in {A, C, G, T}.

Usage

check_and_remove_discarded_variants(
  vcf,
  name_of_vcf = NULL,
  chr_names_to_process = NULL
)

Arguments

vcf

A VCF as a data.frame / data.table.

name_of_vcf

Optional name, used in warning messages.

chr_names_to_process

Optional character vector of chromosome names to keep (overrides the default non-standard-contig filter).

Value

A list with element df, the retained rows of vcf (same class as the input), and, only when at least one row was removed, element discarded.variants, a data.table of the removed rows with an added character column discarded.reason explaining why each row was discarded.