Simple spectra toolbox

A simple R script to compute mutational spectra starting from a MAF file. The MAF file must have the following fields:

• Variant_Type: values SNP, DNP, INS, DEL used in this repo
• Reference_Allele, Tumor_Seq_Allele2: all values used in this repo
• ref_context: 10bp 5' and 10bp 3' of germline reference variant, including the reference allele. this field is 21bp long for SNP, 20 for INS, and 20+ for DELs.

Usage:

maf="CTF001_BMPCs_170_validated_hg38.merged.maf.txt"

Rscript --vanilla src/spectrum.R \
        --maf "${maf}" \
        --home src/ \
        --mutation_type sbs,dbs,id \
        --save all \
        --sample test_id

Options:

• maf: see above. direct from getzlab pipeline
• home: path to spectrum/utils libraries are (in this repo, src)
• mutation_type: comma-separated value list among sbs (single base substitution, understood in a 96- trinucleotidic context), dbs (double base substitution, 78-context), id (small insertions and deletions, 83-context).
• save: comma-separated value list of among pdf (figures in a pdf format, 1 page per mutation_type), and tsv (1 line per maf file, 1 column per context)
• sample: convenient field to add a sample_name as a prefix to exported files and inside the tsv in the sample column