SomaticCombiner: SomaticCombiner

In hubentu/VariantCombiner: Combine VCF variants

SomaticCombiner

Description

To merge two VCFs from different somatic callers.

Usage

SomaticCombiner(
  vcf1,
  vcf2,
  sources,
  GENO = c(GT = 1, DP = 1, AD = 1),
  id_t = "TUMOR",
  id_n = "NORMAL",
  pass_only = FALSE
)

Arguments

vcf1	VCF object or vcf file
vcf2	VCF object or vcf file
sources	The caller of the VCF files.
GENO	The GENO item sources of the mereged VCF. For example c(GT = 1, AD = 2). The vector names are the GENO names and the values are the corresponding index.
id_t	The tumor sample ID.
id_n	The normal/control sample ID.
pass_only	If TRUE, only PASS variants will be merged.

Value

A merged VCF object

hubentu/VariantCombiner documentation built on Dec. 1, 2022, 8:15 a.m.