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lima1 / PureCN

Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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I need advice when there is no normal #373

Open MaryGoAround opened 3 weeks ago

MaryGoAround commented 3 weeks ago

I have targeted DNA sequencing for a tumour and I do not have any normal samples (matched or even non matched)

I am trying this but I get error

 Rscript /R/x86_64-pc-linux-gnu-library/4.4/PureCN/extdata/PureCN.R --out purecn_output --tumor sample_coverage_loess.txt.gz --vcf tumor.vcf.gz --sampleid sample --genome hg38 --post-optimize --force --fun-segmentation Hclust
[1] "folder"
INFO [2024-08-22 16:33:26] Loading PureCN 2.10.0...
Error in .getNormalCoverage(normal.coverage.file) : 
  Need either normalDB or normal.coverage.file
Execution halted

Please give me an advice how to use this software in the case

Thanks a lot

sample_coverage_loess

lima1 commented 2 weeks ago

Hi @MaryGoAround , unfortunately, the software assumes normal samples. We don't use WGS, and for hybrid capture data, it is really difficult to normalize cancer data without normal samples. At least to get it as clean as needed for purity/ploidy determination.

I would check WGS specific software like https://github.com/Wedge-lab/battenberg . It's been a long time since I last used it, so there might be other tools more appropriate for your data.

Sorry that I cannot be more helpful.