ICAMS (version 2.0.7)

ReadAndSplitMutectVCFs: Read and split Mutect VCF files.

Description

Read and split Mutect VCF files.

Usage

ReadAndSplitMutectVCFs(files)

Arguments

files

Character vector of file paths to the Mutect VCF files.

Value

A list with 3 in-memory VCFs and two left-over VCF-like data frames with rows that were not incorporated into the first 3 VCFs, as follows:

1. SBS VCF with only single base substitutions.

2. DBS VCF with only doublet base substitutions as called by Mutect.

3. ID VCF with only small insertions and deletions.

4. other.subs VCF like data.frame with rows for coordinate substitutions involving 3 or more nucleotides, e.g. ACT > TGA or AACT > GGTA.

5. multiple.alternative.alleles VCF like data.frame with rows for variants with multiple alternative alleles, for example ACT mutated to both AGT and ACT at the same position.

See Also

MutectVCFFilesToCatalog

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitMutectVCFs(file)
# }