SBS: List of VCFs with only single base substitutions.
DBS: List of VCFs with only doublet base substitutions as called
by Mutect.
ID: List of VCFs with only small insertions and deletions.
discarded.variants: Non-NULL only if there are variants
that were excluded from the analysis. See the added extra column
discarded.reason for more details.
Arguments
files
Character vector of file paths to the Mutect VCF files.
names.of.VCFs
Optional. Character vector of names of the VCF files.
The order of names in names.of.VCFs should match the order of VCF
file paths in files. If NULL(default), this function will
remove all of the path up to and including the last path separator (if any)
in files and file paths without extensions (and the leading dot)
will be used as the names of the VCF files.
tumor.col.names
Optional. Character vector of column names in VCFs
which contain the tumor sample information. The order of names in
tumor.col.names should match the order of VCFs specified in
files. If tumor.col.names is equal to NA(default),
this function will use the 10th column in all the VCFs to calculate VAFs.
See GetMutectVAF for more details.
suppress.discarded.variants.warnings
Logical. Whether to suppress
warning messages showing information about the discarded variants. Default
is TRUE.