VCFsToID115Catalogs: Create ID (small insertion and deletion) catalog from ID VCFs

In steverozen/ICAMSxtra: ICAMSxtra

Description

Create ID (small insertion and deletion) catalog from ID VCFs

Usage

VCFsToID115Catalogs(
  list.of.vcfs,
  ref.genome,
  region = "unknown",
  flag.mismatches = 0
)

Arguments

list.of.vcfs	List of in-memory ID VCFs. The list names will be the sample ids in the output catalog.
ref.genome	A ref.genome argument as described in ICAMS.
region	A character string acting as a region identifier, one of "genome", "exome".
flag.mismatches	Optional. If > 0, then if there are mismatches to references in the ID (insertion/deletion) VCF, generate messages showing the mismatched rows and continue. Otherwise stop if there are mismatched rows. See AnnotateIDVCF for more details.

Value

A list of two elements. 1st element catalog is the ID (small insertion and deletion) catalog with attributes added. See as.catalog for more details. 2nd element annotated.vcfs is a list of data frames which contain the original VCF with three additional columns seq.context.width, seq.context and ID.class added. The category assignment of each ID mutation in VCF can be obtained from ID.class column.

Note

In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

steverozen/ICAMSxtra documentation built on Feb. 9, 2022, 7:01 a.m.