Convert an annotated indel VCF to a COSMIC 83-category catalog — annot_vcf_to_83

Take an annotated indel VCF data frame (with column COSMIC_83 as produced by indel classification functions) and produce a single-column data frame of mutation counts in the 83-category COSMIC ID classification scheme.

Usage

annot_vcf_to_83_catalog(
  annot_vcf,
  sample_id = "no_sample_id_provided",
  FILTER_PASS = TRUE,
  do_message = FALSE,
  clip_le_9 = TRUE
)

Arguments

annot_vcf: A data frame with at least columns CHROM, POS, ALT, and COSMIC_83. If FILTER_PASS is TRUE, a FILTER column is also required.
sample_id: A character string used as the column name in the returned data frame.
FILTER_PASS: If TRUE, retain only rows where the FILTER column equals "PASS".
do_message: If TRUE, emit diagnostic messages showing row counts at each processing step.
clip_le_9: Only keep variants with "R" <= 9, to approximate PCAWG indel calling.

Value

A single-column data frame with 83 rows (one per COSMIC ID category) and integer mutation counts. Row names are the COSMIC 83 category strings; the column name is sample_id.

Details

The function:

Optionally filters to PASS variants.
Removes duplicate positions (warns if ALT alleles differ).
Tallies counts per COSMIC 83 category and returns a data frame with one row per category (using catalog_row_order()$ID).