How to cite in the manuscript if running PureCN with GATK segmentation

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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How to cite in the manuscript if running PureCN with GATK segmentation #330

Closed WangKang-Leo closed 9 months ago

WangKang-Leo commented 9 months ago

Hi, I recently ran the WES using PureCN, and GATK segmentation was applied. Could you please clarify that GATK represents GATK-gCNV (https://www-nature-com.proxy.kib.ki.se/articles/s41588-023-01449-0) or conventional GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360035535892-Somatic-copy-number-variant-discovery-CNVs-)?

Thanks in advance! Kang

lima1 commented 9 months ago

It's just a wrapper around ModelSegments: https://github.com/lima1/PureCN/blob/devel/R/segmentationGATK4.R#L103C3-L110C38

Coverage was normalized using the Tangent normalization (https://pubmed.ncbi.nlm.nih.gov/36040167/) implemented in PureCN.

WangKang-Leo commented 9 months ago

Thanks for your pormpt reply!

I see now. BTW, maybe it is also great to add GATK-gCNV into PureCN for WES data in the future.

Best regards Kang

lima1 commented 9 months ago

PureCN is a somatic caller, so most of the germline specific functionality we don't really need. But I'll have a look, maybe some ideas we can borrow.