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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.

multiplicity 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.

A hg19 mask is provided in testdata of this package. Please see our dryclean github for masks for hg38.

Parameter	Default value	Description/notes
somatic_snv	NULL	Path to somatic SNV file.
germline_snv	NULL	Path to germline SNV file.
het_pileups_wgs	NULL	Path to het_pileups_wgs file.
jabba_rds	NULL	Path to JaBbA file.
tumor_cbs	NULL	Path to segmented drycleaned coverage file. Overrides tumor_dryclean if provided.
tumor_dryclean	NULL	Path to drycleaned coverage file. If provided, REF/ALT values will be rescaled based on expected base coverage.
dryclean_field		Field in tumor_dryclean gRanges used as rescaled binned coverage.
read_size	151	Estimated average read size (default for Illumina sequencers).
tumor_name	NULL	Expected tumor sample name as annotated in the VCF.
normal_name	NULL	Expected normal sample name as annotated in the VCF.
mask	NULL	Loci within provided mask gRanges will be excluded from analysis.
inferred_sex	NA	Enum of ["M", "F"] indicating the inferred/true patient sex. If not provided, it will be inferred from coverage/JaBbA graph.
tau_in_gamma		Use tau (TRUE) versus tau_hat (FALSE) in computation of gamma. Note: tau_hat uses the average copy number of loci, while tau is simply ploidy.
filterpass		Process only variants with FILTER == PASS?
purity		Purity of the input jabba_rds. Optional if gGraph metadata includes purity.
ploidy		Ploidy of the input jabba_rds. Optional if gGraph metadata includes ploidy.
snpeff_path	/path/to/snpeff	Path to the unzipped SnpEff toolkit.
verbose	TRUE	Enable verbose output.

License

MIT