search

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
100 stars 37 forks source link

Feature request: annotate each variant with the context #15

Closed itsvenu closed 5 years ago

itsvenu commented 5 years ago

Hi @ebergstr,

Thanks for the amazing tool. I was just thinking is it possible (with current implementation or with some modifications) to annotate each variant in the input files with the context (for SBS, DBS, ID) and output a text file (may include chr, position, ref, alt, context, sampleID).

IMO, there will be several use cases for integrative analysis with this data e.g. one can calculate overrepresentation of different contexts in certain genomic loci such as enhancers or open chromatin regions.

Any help would be appreciated.

Thank you.

ebergstr commented 5 years ago

This is implemented in the seqInfo=True parameter (more information provided on the wiki page