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Introduction

A simplistic transformation of counts to multiplicity as outlined in our published works: JaBbA v1 Choo et al. & JaBbA v0 Hadi et al.. Please see Supplementary Note 2 and STAR Methods, respectively, in these publications for full details on this derivation.

SNVplicity is an R library to convert counts from mutation-caller derived .vcfs to total copies given known purity, ploidy, and consitutional discerned copy number as ideally determined by JaBbA.

Usage

Either somatic_snv or germline_snv must be provided. Typically, mutation callers will deposit alt/ref counts per tumor/normal pair in a single file.

As such, we suggest you provide the expected define column names for the tumor and normal sample (tumor_name & normal_name, respectively). By default, if a single sample is contained in the provided vcf, that sample will be assumed to be tumor. If two samples are contained in the provided vcf, the second column will be defined to be the tumor whereas the first will be defined as the normal.

Parameter	Default value	Description/notes
somatic_snv	NULL	Path to somatic vcf.
germline_snv	NULL	Path to germline vcf.
jabba_rds		JaBbA-derived gGraph or jabba.simple.rds
snpeff_path	/path/to/snpeff	Path to unzipped/untarred SnpEff directory, containing discrete scripts; importantly, SnpSift & vcfEffOnePerLine.pl
tumor_name	NULL
normal_name	NULL
verbose	TRUE	Informative logging of function?

License

MIT