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AlexandrovLab / SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
BSD 2-Clause "Simplified" License
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identify SBS4 for tobacco smoking #152

Closed Dhwani-2410 closed 1 year ago

Dhwani-2410 commented 1 year ago

Hello,

I have a VCF file and I would like to know:- 1) Which among the 96SBS is more prominent in the current VCF data based on the classification of SBS by the COSMIC database? 2) Plots of specific SBS4 COSMIC signatures.

These are the commands that i had ran

from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
matrices = matGen.SigProfilerMatrixGeneratorFunc("Demo1","GRCh37","/home/dhwani/Desktop/VCFInput/",exome=False, bed_file=None, chrom_based=False, plot=True, tsb_stat=False, seqInfo=True)

from SigProfilerExtractor import sigpro as sig
sig.sigProfilerExtractor("matrix","Demo2","/home/dhwani/Desktop/VCFInput/output/SBS/Demo1.SBS6.all",reference_genome="GRCh37",minimum_signatures=1,maximum_signatures=200,nmf_replicates=100,cpu=-1)

In the second command, I want to get SigprofileExtrator only for SBS4(tobacco smoking). But the output from the previous command only consists of SBS6, SBS26, and SBS96.SBS384,SBS1536 and SBS6144

mdbarnesUCSD commented 1 year ago

Hi @Dhwani-2410,

To clarify, there is a difference between COSMIC signature SBS4 and the different mutational contexts. Here are resources for each, COSMIC signatures (ie SBS4) and mutational contexts.