Hi everyone, I'm looking to run just LILAC from the oncoanalyser suite. I currently have 36 tumor–normal paired WES DNA samples, with somatic variants called using a consensus approach and copy number variants generated with CNVkit. I noticed on the GitHub that LILAC was originally designed to take SAGE somatic mutation output and PURPLE allele-specific CNV calls as input, but that other input sources are also supported. I'm wondering: • What are the implications of using alternative somatic variant and CNV callers? • Are there any best practices or known limitations when using non-SAGE or non-PURPLE inputs with LILAC? Any guidance or examples from others who have used custom inputs would be greatly appreciated.

I think this might be more of a question for the WiGiTS team (via https://github.com/hartwigmedical/hmftools/tree/master/lilac) than oncoanalyser; we've not tested a lot of the toolkit in isolation other than support for different aligners and to some extent reference genomes, but the Hartwig team might have.

Hey Oliver, Thanks so much for your response will look into this.