Modify ichorCNA.snakefile for Panel of Normal (PoN)

[wjaratlerdsiri]

Dear Gavin,

I am using your excellent snakemake workflow successfully and like to include PoN in ichorCNA.snakefile.

Can I just simply add '--normalPanel /path/to/${pon}' in Line 70 of the ichorCNA.snakefile script?

Ex. "Rscript {params.rscript} --libdir {params.libdir} --id {params.id} --WIG {input.tum} --gcWig {params.gcwig} --mapWig {params.mapwig} --NORMWIG {input.norm} --ploidy \"{params.ploidy}\" --normal \"{params.normal}\" --maxCN {params.maxCN} --includeHOMD {params.includeHOMD} --genomeStyle {params.genomeStyle} --chrs \"{params.chrs}\" --estimateNormal {params.estimateNormal} --estimatePloidy {params.estimatePloidy} --estimateScPrevalence {params.estimateClonality} --scStates \"{params.scStates}\" --centromere {params.centromere} --exons.bed {params.exons} --txnE {params.txnE} --txnStrength {params.txnStrength} --fracReadsInChrYForMale {params.fracReadsChrYMale} --plotFileType {params.plotFileType} --plotYLim \"{params.plotYlim}\" --outDir {params.outDir} --normalPanel /path/to/${pon} > {log} 2> {log}"

I could try the sample PoN, but there is no 200bp-binned PoN file. Thank you in advance for your technical advice.

James

[gavinha]

Hi @wjaratlerdsiri

Unfortunately, we do not have a 200bp bin size PoN. If you have a set of normal samples, you can try to create your own. Please refer to the ichorCNA GitHub repo for more information.

https://github.com/broadinstitute/ichorCNA/wiki/Create-Panel-of-Normals

Best, Gavin