R: Split each VCF into SBS, DBS, and ID VCFs (plus VCF-like data...

SplitListOfVCFs

R Documentation

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

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

SplitListOfVCFs(
  list.of.vcfs,
  variant.caller,
  max.vaf.diff = 0.02,
  num.of.cores = 1,
  suppress.discarded.variants.warnings = TRUE
)

`list.of.vcfs`	List of VCFs as in-memory data.frames.
`variant.caller`	Name of the variant caller that produces the VCF, can be either `"strelka"`, `"mutect"`, `"freebayes"` or `"unknown"`. If variant caller is `"mutect"`, do not merge SBSs into DBS.
`max.vaf.diff`	The maximum difference of VAF, default value is 0.02. If the absolute difference of VAFs for adjacent SBSs is bigger than `max.vaf.diff`, then these adjacent SBSs are likely to be "merely" asynchronous single base mutations, opposed to a simultaneous doublet mutation or variants involving more than two consecutive bases.
`num.of.cores`	The number of cores to use. Not available on Windows unless `num.of.cores = 1`.
`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.