from genomic variations in vcf filesbioconductor-mutationalpatternsr-optparser-rjsonr-nmfr-gridextrabioconductor-bsgenome.hsapiens.ucsc.hg38bioconductor-bsgenome.hsapiens.1000genomes.hs37d5bioconductor-bsgenome.hsapiens.ucsc.hg19bioconductor-bsgenome.hsapiens.ncbi.grch38set_spectrum['choices'] == "yes"set_denovo['choices'] == "yes"set_denovo['choices'] == "yes"set_cosmic['choices'] == "yes"rdata_out
**What it does**
Takes as inputs
* a collection of n vcf files corresponding to n samples.
* a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
* the number of cosmic signatures to decompose mutational patterns of samples
This tool returns a pdf file with the visualisation :
* the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
* the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
* the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
* a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
* pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern
.. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
10.18129/B9.bioc.MutationalPatterns10.1186/s13073-018-0539-010.1038/nature12477