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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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Use PureCN in combination with HRDetect #216

Closed kristianunger closed 2 years ago

kristianunger commented 2 years ago

Describe the issue Missing information in output/question about possibility to create output to be used in HRDetect

I am using PureCN for all my tumor WES analyses and now would like to apply the HRDetect pipeline https://github.com/eyzhao/hrdetect-pipeline and work out HRD scores. However, HRDetect requires the input as described here

https://github.com/eyzhao/hrdetect-pipeline#example-pipeline

so, for instance for LOH the LOH type is required. Is it possible to generate the LOH-types using the categories?

ASCNA: Allele-specific copy number amplification BCNA: Balanced copy number amplification HET: Heterozygous (normal) NLOH: Neutral LOH (loss of heterozygosity, but 2 copies present) DLOH: Deletion LOH ALOH: Amplification LOH

Any help would be appreciated!

lima1 commented 2 years ago

Yep, all you need is in the loh output file from PureCN.R. LOH is when M = 0 (M = minor copy number). So the different types are based on the C column (total copy number, minor + major copy number = total copy number, minor <= major). C = 2: NLOH C = 1 or 0: DLOH C > 2: ALOH BCNA: M > 0; C = M * 2; C > 2 ASCNA: M > 0; C > 2 HET: M= 1; C = 2

Those classifications are sensitive to ploidy. So important to check cases with high ploidy if they are true genome duplications.

kristianunger commented 2 years ago

Thank you so much! I will try out and let you know how if it worked.