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morrislab / TrackSig

A framework to infer mutational signatures in cancer over time
MIT License
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Effect of using reference other than hg19 in getMutationTypes.pl #11

Open MUppal opened 4 years ago

MUppal commented 4 years ago

Quick question here regarding extending TrackSig beyond the hg19 reference build. In src/getMutationTypes.pl, line 16 has the explicit delineation of using hg19: my %fastaHandles = ("path" => "annotation/hg19/");

My question is, could other reference files be used, like hg38, with the corresponding set of chromosomes used, and simple alteration of line 16? Would this result in any meaningful change of performance in TrackSig? Or is TrackSig meant to be used only with hg19-aligned genomes?

YuliaRubanova commented 4 years ago

Hi! In theory, TrackSig should still run after changing hg19 to hg38. However, the signature definitions that we use were derived from tumours with hg19 calls.

The definitions of COSMIC mutational signatures also should be agnostic to the version of the genome: https://cancer.sanger.ac.uk/cosmic/signatures?genome=38