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Convert an annotated indel VCF to a Koh 476-category catalog

Source: R/annot_vcf_to_476_catalog.R
annot_vcf_to_476_catalog.Rd

Take an annotated indel VCF data frame (with columns Koh_476 and R as produced by indel classification functions) and produce a single-column data frame of mutation counts in the 476-category Koh classification scheme.

Usage

annot_vcf_to_476_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, Koh_476, and R (repeat count). 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 476 rows (one per Koh category) and integer mutation counts. Row names are the Koh 476 category strings; the column name is sample_id.

Details

The function:

  1. Optionally filters to PASS variants.

  2. Removes duplicate positions (warns if ALT alleles differ).

  3. Collapses single-base indels with repeat count \(\ge 9\) into an "R(9,)" bin.

  4. Tallies counts per Koh 476 category and returns a data frame with one row per category (using catalog_row_order()$ID476).