ICAMS (version 3.0.11)

StandardChromNameNew: Standardize the chromosome name annotations for a data frame.

Description

Standardize the chromosome name annotations for a data frame.

Usage

StandardChromNameNew(df, name.of.VCF = NULL)

Value

A list with the elements

• df a data frame with variants that had "legal" chromosome names (see below for illegal chromosome names).

• discarded.variants: Non-NULL only if there are variants with illegal chromosome names; these are names that contain the strings "GL", "KI", "random", "Hs", "M", "JH", "fix", "alt".

Arguments

df

An in-memory data.frame representing a VCF.

name.of.VCF

Name of the VCF file.