ICAMS: SplitListOfMutectVCFs – R documentation

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SplitListOfMutectVCFs

Split each Mutect VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)

Split each Mutect VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)

SplitListOfMutectVCFs(
  list.of.vcfs,
  suppress.discarded.variants.warnings = TRUE
)

`list.of.vcfs`	List of VCFs as in-memory data.frames.
`suppress.discarded.variants.warnings`	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

A list containing the following objects:

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.

In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release