How to deal with 'Intron' and 'IGR' variants from WES data when fitting signatures?

UMCUGenetics / MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

MIT License

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How to deal with 'Intron' and 'IGR' variants from WES data when fitting signatures? #68

Closed lincj1994 closed 3 years ago

lincj1994 commented 3 years ago

Hi. I want to fit signatures for WES sequencing data. But I dont know how to deal with 'Intron' and 'IGR' variants for WES data when fitting signatures. (About 40 percent of the variants were Intron). Keep it or remove it. Thank you

FreekManders commented 3 years ago

Signature analysis is often done on WGS data, so I think it is fine to keep all the variants in this case.